From 2b7fef2e0699efbdc5f9648fc8ec2a494cd1e963 Mon Sep 17 00:00:00 2001 From: rori <6863459+RoriCremer@users.noreply.github.com> Date: Thu, 10 Jun 2021 12:57:31 -0400 Subject: [PATCH 01/73] init wdl to make sites only vcfs from extracted cohort vcfs --- .../wdl/GvsSitesOnlyVCF.example.inputs.json | 5 + scripts/variantstore/wdl/GvsSitesOnlyVCF.wdl | 98 +++++++++++++++++++ 2 files changed, 103 insertions(+) create mode 100644 scripts/variantstore/wdl/GvsSitesOnlyVCF.example.inputs.json create mode 100644 scripts/variantstore/wdl/GvsSitesOnlyVCF.wdl diff --git a/scripts/variantstore/wdl/GvsSitesOnlyVCF.example.inputs.json b/scripts/variantstore/wdl/GvsSitesOnlyVCF.example.inputs.json new file mode 100644 index 00000000000..36e105fa4bb --- /dev/null +++ b/scripts/variantstore/wdl/GvsSitesOnlyVCF.example.inputs.json @@ -0,0 +1,5 @@ +{ + "GvsSitesOnlyVCF.gvs_extract_cohort_filtered_vcfs": ["gs://broad-dsp-spec-ops/scratch/rcremer/Nirvana/Data/anvil_expected.vcf"], + "GvsSitesOnlyVCF.output_sites_only_file_name": "hello_did_I_sites_only", + "GvsSitesOnlyVCF.output_merged_file_name": "hello_did_I_merge" +} diff --git a/scripts/variantstore/wdl/GvsSitesOnlyVCF.wdl b/scripts/variantstore/wdl/GvsSitesOnlyVCF.wdl new file mode 100644 index 00000000000..0d53fc87ec9 --- /dev/null +++ b/scripts/variantstore/wdl/GvsSitesOnlyVCF.wdl @@ -0,0 +1,98 @@ +version 1.0 + +workflow GvsSitesOnlyVCF { + input { + Array[File] gvs_extract_cohort_filtered_vcfs + String output_sites_only_file_name + String output_merged_file_name + File? gatk_override + } + + scatter(i in range(length(gvs_extract_cohort_filtered_vcfs)) ) { + call SitesOnlyVcf { + input: + vcf_bgz_gts = gvs_extract_cohort_filtered_vcfs[i], + output_filename = "${output_sites_only_file_name}_${i}.sites_only.vcf.gz", + } + } + + call MergeVCFs { + input: + input_vcfs = SitesOnlyVcf.output_vcf, + input_vcf_indices = SitesOnlyVcf.output_vcf_index, + output_merged_file_name = output_merged_file_name, + } +} + +################################################################################ +task SitesOnlyVcf { + input { + File vcf_bgz_gts + String output_filename + } + # this needs to be array-ized + parameter_meta { + vcf_bgz_gts: {localization_optional: true} + } + command <<< + set -e + gatk --java-options "-Xmx2048m" \ + SelectVariants \ + -V ~{vcf_bgz_gts} \ + --exclude-filtered \ + --sites-only-vcf \ + -O ~{output_filename} + + tabix ~{output_filename} + + >>> + # add an indexing bit here? + + # ------------------------------------------------ + # Runtime settings: + runtime { + #docker:"broadinstitute/gatk:4.2.0.0" + docker: "us.gcr.io/broad-dsde-methods/broad-gatk-snapshots:varstore_d8a72b825eab2d979c8877448c0ca948fd9b34c7_change_to_hwe" + memory: "3 GB" + cpu: "1" + disks: "local-disk 100 HDD" + } + + # ------------------------------------------------ + # Outputs: + + output { + File output_vcf="~{output_filename}" + File output_vcf_index = "~{output_filename}.tbi" + } +} + +task MergeVCFs { + input { + Array[File] input_vcfs + Array[File] input_vcf_indices + String output_merged_file_name + } + String output_vcf = basename(output_merged_file_name) + ".vcf.gz" + String output_vcf_idx = basename(output_vcf) + ".tbi" + command <<< + set -e + gatk --java-options "-Xmx2048m" MergeVcfs -I ~{sep=' -I ' input_vcfs} -O ~{output_vcf} + >>> + runtime { + docker: "broadinstitute/gatk:4.2.0.0" + memory: "3 GB" + cpu: "1" + disks: "local-disk 100 HDD" + } + output { + File merged_vcf = "~{output_vcf}" + File merged_vcf_idx = "~{output_vcf_idx}" + } +} + + + + + + From 41d3ef8554a9ea9c215bb95314e09fef429149c0 Mon Sep 17 00:00:00 2001 From: rori <6863459+RoriCremer@users.noreply.github.com> Date: Thu, 10 Jun 2021 16:44:11 -0400 Subject: [PATCH 02/73] init schema --- .../variantstore/wdl/schemas/vat_schema.json | 109 ++++++++++++++++++ 1 file changed, 109 insertions(+) create mode 100644 scripts/variantstore/wdl/schemas/vat_schema.json diff --git a/scripts/variantstore/wdl/schemas/vat_schema.json b/scripts/variantstore/wdl/schemas/vat_schema.json new file mode 100644 index 00000000000..e1a93f15fd6 --- /dev/null +++ b/scripts/variantstore/wdl/schemas/vat_schema.json @@ -0,0 +1,109 @@ +[ + { + "description": "Variant ID", + "name": "vid", + "type": "String", + "mode": "Required" + }, + { + "description": "Transcript ID", + "name": "transcript", + "type": "String", + "mode": "Nullable" + }, + { + "description": "Contig names match the hg38 reference", + "name": "contig", + "type": "String", + "mode": "Nullable" + }, + + + + + + + + + + + + { + "description": "[DESCRIPTION]", + "name": "alt", + "type": "String", + "mode": "Required" + }, + { + "description": "[DESCRIPTION]", + "name": "AS_RAW_MQ", + "type": "String", + "mode": "Required" + }, + { + "description": "[DESCRIPTION]", + "name": "AS_RAW_MQRankSum", + "type": "String", + "mode": "Nullable" + }, + { + "description": "[DESCRIPTION]", + "name": "AS_QUALapprox", + "type": "String", + "mode": "Required" + }, + { + "description": "[DESCRIPTION]", + "name": "AS_RAW_ReadPosRankSum", + "type": "String", + "mode": "Nullable" + }, + { + "description": "[DESCRIPTION]", + "name": "AS_SB_TABLE", + "type": "String", + "mode": "Required" + }, + { + "description": "[DESCRIPTION]", + "name": "AS_VarDP", + "type": "String", + "mode": "Required" + }, + { + "description": "[DESCRIPTION]", + "name": "call_GT", + "type": "String", + "mode": "Required" + }, + { + "description": "[DESCRIPTION]", + "name": "call_AD", + "type": "String", + "mode": "Nullable" + }, + { + "description": "[DESCRIPTION]", + "name": "call_GQ", + "type": "Integer", + "mode": "Required" + }, + { + "description": "[DESCRIPTION]", + "name": "call_PGT", + "type": "String", + "mode": "Nullable" + }, + { + "description": "[DESCRIPTION]", + "name": "call_PID", + "type": "String", + "mode": "Nullable" + }, + { + "description": "[DESCRIPTION]", + "name": "call_PL", + "type": "String", + "mode": "Required" + } +] From 4d07f832ad622312b5ed2cf3109e3297c340cabf Mon Sep 17 00:00:00 2001 From: rori <6863459+RoriCremer@users.noreply.github.com> Date: Thu, 10 Jun 2021 16:44:31 -0400 Subject: [PATCH 03/73] just get the wdl working --- scripts/variantstore/wdl/GvsSitesOnlyVCF.wdl | 69 +++----------------- 1 file changed, 10 insertions(+), 59 deletions(-) diff --git a/scripts/variantstore/wdl/GvsSitesOnlyVCF.wdl b/scripts/variantstore/wdl/GvsSitesOnlyVCF.wdl index 0d53fc87ec9..e763391c48a 100644 --- a/scripts/variantstore/wdl/GvsSitesOnlyVCF.wdl +++ b/scripts/variantstore/wdl/GvsSitesOnlyVCF.wdl @@ -1,28 +1,18 @@ version 1.0 - workflow GvsSitesOnlyVCF { input { - Array[File] gvs_extract_cohort_filtered_vcfs + File gvs_extract_cohort_filtered_vcf String output_sites_only_file_name - String output_merged_file_name File? gatk_override } - scatter(i in range(length(gvs_extract_cohort_filtered_vcfs)) ) { - call SitesOnlyVcf { - input: - vcf_bgz_gts = gvs_extract_cohort_filtered_vcfs[i], - output_filename = "${output_sites_only_file_name}_${i}.sites_only.vcf.gz", - } - } + call SitesOnlyVcf { + input: + vcf_bgz_gts = gvs_extract_cohort_filtered_vcf, + output_filename = "${output_sites_only_file_name}.sites_only.vcf.gz", + } - call MergeVCFs { - input: - input_vcfs = SitesOnlyVcf.output_vcf, - input_vcf_indices = SitesOnlyVcf.output_vcf_index, - output_merged_file_name = output_merged_file_name, } -} ################################################################################ task SitesOnlyVcf { @@ -30,69 +20,30 @@ task SitesOnlyVcf { File vcf_bgz_gts String output_filename } - # this needs to be array-ized - parameter_meta { - vcf_bgz_gts: {localization_optional: true} - } + String output_vcf_idx = basename(output_filename) + ".tbi" # or will this be .idx if from .vcf.gz command <<< set -e gatk --java-options "-Xmx2048m" \ SelectVariants \ -V ~{vcf_bgz_gts} \ --exclude-filtered \ - --sites-only-vcf \ + --sites-only-vcf-output \ -O ~{output_filename} - - tabix ~{output_filename} - >>> - # add an indexing bit here? - # ------------------------------------------------ # Runtime settings: runtime { - #docker:"broadinstitute/gatk:4.2.0.0" - docker: "us.gcr.io/broad-dsde-methods/broad-gatk-snapshots:varstore_d8a72b825eab2d979c8877448c0ca948fd9b34c7_change_to_hwe" + docker: "broadinstitute/gatk:4.2.0.0" memory: "3 GB" cpu: "1" disks: "local-disk 100 HDD" } - # ------------------------------------------------ # Outputs: - output { File output_vcf="~{output_filename}" - File output_vcf_index = "~{output_filename}.tbi" - } -} - -task MergeVCFs { - input { - Array[File] input_vcfs - Array[File] input_vcf_indices - String output_merged_file_name - } - String output_vcf = basename(output_merged_file_name) + ".vcf.gz" - String output_vcf_idx = basename(output_vcf) + ".tbi" - command <<< - set -e - gatk --java-options "-Xmx2048m" MergeVcfs -I ~{sep=' -I ' input_vcfs} -O ~{output_vcf} - >>> - runtime { - docker: "broadinstitute/gatk:4.2.0.0" - memory: "3 GB" - cpu: "1" - disks: "local-disk 100 HDD" - } - output { - File merged_vcf = "~{output_vcf}" - File merged_vcf_idx = "~{output_vcf_idx}" + File output_vcf_idx="~{output_vcf_idx}" } } - - - - From 275338240350a9d941fe8b0e4e0d3840c98cea49 Mon Sep 17 00:00:00 2001 From: rori <6863459+RoriCremer@users.noreply.github.com> Date: Fri, 11 Jun 2021 16:43:27 -0400 Subject: [PATCH 04/73] update schema to have all NIRVANA selected annotations --- .../variantstore/wdl/schemas/vat_schema.json | 259 ++++++++++++++---- 1 file changed, 202 insertions(+), 57 deletions(-) diff --git a/scripts/variantstore/wdl/schemas/vat_schema.json b/scripts/variantstore/wdl/schemas/vat_schema.json index e1a93f15fd6..42935ea18a6 100644 --- a/scripts/variantstore/wdl/schemas/vat_schema.json +++ b/scripts/variantstore/wdl/schemas/vat_schema.json @@ -1,12 +1,12 @@ [ { - "description": "Variant ID", + "description": "Variant ID. Unique string for identifying a variant (as produced by NIRVANA based on a spec from Broad Institute)", "name": "vid", "type": "String", "mode": "Required" }, { - "description": "Transcript ID", + "description": "Transcript ID. Null indicates that this variant does not overlap any transcripts", "name": "transcript", "type": "String", "mode": "Nullable" @@ -17,93 +17,238 @@ "type": "String", "mode": "Nullable" }, - - - - - - - - - - - - { - "description": "[DESCRIPTION]", - "name": "alt", - "type": "String", - "mode": "Required" - }, - { - "description": "[DESCRIPTION]", - "name": "AS_RAW_MQ", - "type": "String", +{ + "description": "Must be positive. Exact position for a SNP and the position before the alteration in an indel", + "name": "position", + "type": "Integer", "mode": "Required" }, { - "description": "[DESCRIPTION]", - "name": "AS_RAW_MQRankSum", + "description": "base(s). This should always be one base for SNPs and insertions. More than one base for deletions", + "name": "ref_allele", "type": "String", "mode": "Nullable" }, { - "description": "[DESCRIPTION]", - "name": "AS_QUALapprox", - "type": "String", - "mode": "Required" - }, - { - "description": "[DESCRIPTION]", - "name": "AS_RAW_ReadPosRankSum", + "description": "base(s). This should always be one base for SNPs and deletions. More than one base for insertions", + "name": "alt_allele", "type": "String", "mode": "Nullable" }, { - "description": "[DESCRIPTION]", - "name": "AS_SB_TABLE", + "description": "Gene symbol. A variant can have more than one associated gene symbol, since about 3% of genes do overlap", + "name": "gene_symbol", "type": "String", - "mode": "Required" + "mode": "Nullable" }, { - "description": "[DESCRIPTION]", - "name": "AS_VarDP", + "description": "", + "name": "transcript _source", "type": "String", - "mode": "Required" + "mode": "Nullable" }, { - "description": "[DESCRIPTION]", - "name": "call_GT", + "description": "HGVS p. nomenclature; Amino acid change", + "name": "aa_change", "type": "String", - "mode": "Required" + "mode": "Nullable" }, { - "description": "[DESCRIPTION]", - "name": "call_AD", + "description": "Amino acid change type", + "name": "consequence", "type": "String", "mode": "Nullable" }, { - "description": "[DESCRIPTION]", - "name": "call_GQ", - "type": "Integer", - "mode": "Required" - }, - { - "description": "[DESCRIPTION]", - "name": "call_PGT", + "description": "HGVS c. nomenclature; DNA change", + "name": "dna_change", "type": "String", "mode": "Nullable" }, { - "description": "[DESCRIPTION]", - "name": "call_PID", + "description": "DNA change type (HGVS)", + "name": "variant_type", "type": "String", "mode": "Nullable" }, + { + "description": "Exon number", + "name": "exon_number", + "type": "String", + "mode": "Nullable" + }, + { + "description": "Intron number", + "name": "intron_number", + "type": "String", + "mode": "Nullable" + }, + { + "description": "HGVS g. nomenclature Variant location", + "name": "genomic_location", + "type": "String", + "mode": "Nullable" + }, + { + "description": "Splice site distance for introns Will be a positive or negative integer", + "name": "splice_distance", + "type": "String", + "mode": "Nullable" + }, + { + "description": "rsID", + "name": "dbsnp_rsid", + "type": "String", + "mode": "Nullable" + }, + { + "description": "Entrez/NCBI ID", + "name": "entrez_gene_id", + "type": "String", + "mode": "Nullable" + }, + { + "description": "HGNC ID", + "name": "hgnc_gene_id", + "type": "String", + "mode": "Nullable" + }, + { + "description": "OMIM ID", + "name": "gene_omim_id", + "type": "Integer", + "mode": "Nullable" + }, + { + "description": "Primary Transcript ID", + "name": "is_canonical_transcript", + "type": "String", + "mode": "Nullable" + }, + { + "description": "gnomAD: 'Total' frequency", + "name": "gnomad_all_af", + "type": "Float", + "mode": "Nullable" + }, + { + "description": "gnomAD: 'Total' allele count", + "name": "gnomad_all_ac", + "type": "Integer", + "mode": "Nullable" + }, + { + "description": "gnomAD: 'Total' allele number", + "name": "gnomad_all_an", + "type": "Integer", + "mode": "Nullable" + }, + { + "description": "gnomAD: Max subpopulation frequency", + "name": "gnomad_max_af", + "type": "Float", + "mode": "Nullable" + }, + { + "description": "gnomAD: Max subpopulation count", + "name": "gnomad_max_ac", + "type": "Integer", + "mode": "Nullable" + }, + { + "description": "gnomAD: Max subpopulation number", + "name": "gnomad_max_an", + "type": "Integer", + "mode": "Nullable" + }, + { + "description": "gnomAD: Max subpopulation ethnicity", + "name": "gnomad_max_subpop", + "type": "String", + "mode": "Nullable" + }, + { + "description": "REVEL", + "name": "revel", + "type": "String", + "mode": "Nullable" + }, + { + "description": "Slice AI", + "name": "splice_ai_acceptor_gain_score", + "type": "Float", + "mode": "Nullable" + }, + { + "description": "Slice AI", + "name": "splice_ai_acceptor_gain_distance", + "type": "Integer", + "mode": "Nullable" + }, + { + "description": "Slice AI", + "name": "splice_ai_acceptor_loss_score", + "type": "Float", + "mode": "Nullable" + }, + { + "description": "Slice AI", + "name": "splice_ai_acceptor_loss_distance", + "type": "Integer", + "mode": "Nullable" + }, + { + "description": "Slice AI", + "name": "splice_ai_donor_gain_score", + "type": "Float", + "mode": "Nullable" + }, + { + "description": "Slice AI", + "name": "splice_ai_donor_gain_distance", + "type": "Integer", + "mode": "Nullable" + }, + { + "description": "Slice AI", + "name": "splice_ai_donor_loss_score", + "type": "Float", + "mode": "Nullable" + }, + { + "description": "Slice AI", + "name": "splice_ai_donor_loss_distance", + "type": "Integer", + "mode": "Nullable" + }, + { + "description": "OMIM Disease ID", + "name": "omim_phenotypes_id", + "type": "Integer", + "mode": "Repeated" + }, + { + "description": "OMIM Disease Name", + "name": "omim_phenotypes_name", + "type": "String", + "mode": "Repeated" + }, + { + "description": "ClinVar Classification", + "name": "clinvar_classification", + "type": "String", + "mode": "Nullable" + }, + { + "description": "ClinVar Classification Date", + "name": "clinvar_last_updated", + "type": "Date", + "mode": "Nullable" + }, { - "description": "[DESCRIPTION]", - "name": "call_PL", + "description": "ClinVar Disease Name", + "name": "clinvar_phenotype", "type": "String", - "mode": "Required" + "mode": "Repeated" } ] From ca058c58b8cb1c66ef342f8250ad9179465597cb Mon Sep 17 00:00:00 2001 From: rori <6863459+RoriCremer@users.noreply.github.com> Date: Fri, 11 Jun 2021 16:44:30 -0400 Subject: [PATCH 05/73] add tarball of sources to example input --- scripts/variantstore/wdl/GvsSitesOnlyVCF.example.inputs.json | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/scripts/variantstore/wdl/GvsSitesOnlyVCF.example.inputs.json b/scripts/variantstore/wdl/GvsSitesOnlyVCF.example.inputs.json index 36e105fa4bb..c209b93c4d4 100644 --- a/scripts/variantstore/wdl/GvsSitesOnlyVCF.example.inputs.json +++ b/scripts/variantstore/wdl/GvsSitesOnlyVCF.example.inputs.json @@ -1,5 +1,7 @@ { "GvsSitesOnlyVCF.gvs_extract_cohort_filtered_vcfs": ["gs://broad-dsp-spec-ops/scratch/rcremer/Nirvana/Data/anvil_expected.vcf"], "GvsSitesOnlyVCF.output_sites_only_file_name": "hello_did_I_sites_only", - "GvsSitesOnlyVCF.output_merged_file_name": "hello_did_I_merge" + "GvsSitesOnlyVCF.output_merged_file_name": "hello_did_I_merge", + "GvsSitesOnlyVCF.output_annotated_file_name": "hello_did_I_annotate", + "GvsSitesOnlyVCF.nirvana_data_directory": "gs://broad-dsp-spec-ops/scratch/rcremer/Nirvana/NirvanaData.tar.gz" } From 4ec5e2b40781419c1fa79b5c86e99234bfc309cf Mon Sep 17 00:00:00 2001 From: rori <6863459+RoriCremer@users.noreply.github.com> Date: Fri, 11 Jun 2021 20:16:53 -0400 Subject: [PATCH 06/73] add annotations --- scripts/variantstore/wdl/GvsSitesOnlyVCF.wdl | 112 +++++++++++++++++-- 1 file changed, 105 insertions(+), 7 deletions(-) diff --git a/scripts/variantstore/wdl/GvsSitesOnlyVCF.wdl b/scripts/variantstore/wdl/GvsSitesOnlyVCF.wdl index e763391c48a..671072c9e5c 100644 --- a/scripts/variantstore/wdl/GvsSitesOnlyVCF.wdl +++ b/scripts/variantstore/wdl/GvsSitesOnlyVCF.wdl @@ -1,18 +1,36 @@ version 1.0 workflow GvsSitesOnlyVCF { input { - File gvs_extract_cohort_filtered_vcf + Array[File] gvs_extract_cohort_filtered_vcfs String output_sites_only_file_name + String output_merged_file_name + String output_annotated_file_name + File nirvana_data_directory File? gatk_override } - call SitesOnlyVcf { - input: - vcf_bgz_gts = gvs_extract_cohort_filtered_vcf, - output_filename = "${output_sites_only_file_name}.sites_only.vcf.gz", - } + scatter(i in range(length(gvs_extract_cohort_filtered_vcfs)) ) { + call SitesOnlyVcf { + input: + vcf_bgz_gts = gvs_extract_cohort_filtered_vcfs[i], + output_filename = "${output_sites_only_file_name}_${i}.sites_only.vcf.gz", + } + } + + call MergeVCFs { # why are we merging before annotating? couldn't we keep them separate? + input: + input_vcfs = SitesOnlyVcf.output_vcf, + input_vcf_indices = SitesOnlyVcf.output_vcf_idx, + output_merged_file_name = output_merged_file_name, + } + call AnnotateVCF { + input: + input_vcf = MergeVCFs.merged_vcf, + output_annotated_file_name = output_annotated_file_name, + nirvana_data_tar = nirvana_data_directory } +} ################################################################################ task SitesOnlyVcf { @@ -20,7 +38,7 @@ task SitesOnlyVcf { File vcf_bgz_gts String output_filename } - String output_vcf_idx = basename(output_filename) + ".tbi" # or will this be .idx if from .vcf.gz + String output_vcf_idx = basename(output_filename) + ".tbi" # or will this be .idx if from .vcf.gz? command <<< set -e gatk --java-options "-Xmx2048m" \ @@ -46,4 +64,84 @@ task SitesOnlyVcf { } } +task MergeVCFs { + input { + Array[File] input_vcfs + Array[File] input_vcf_indices + String output_merged_file_name + } + String output_vcf = basename(output_merged_file_name) + ".vcf.gz" + String output_vcf_idx = basename(output_vcf) + ".tbi" + command <<< + set -e + gatk --java-options "-Xmx2048m" \ + MergeVcfs -I ~{sep=' -I ' input_vcfs} -O ~{output_vcf} + + >>> + # ------------------------------------------------ + # Runtime settings: + runtime { + docker: "broadinstitute/gatk:4.2.0.0" + memory: "3 GB" + cpu: "1" + disks: "local-disk 100 HDD" + } + # ------------------------------------------------ + # Outputs: + output { + File merged_vcf = "~{output_vcf}" + File merged_vcf_idx = "~{output_vcf_idx}" + } +} + +task AnnotateVCF { + input { + File input_vcf + String output_annotated_file_name + File nirvana_data_tar + } + String annotation_json_name = basename(output_annotated_file_name) + ".json.gz" + String annotation_json_name_jsi = annotation_json_name + ".jsi" + + String nirvana_location = "/opt/nirvana/Nirvana.dll" + String path = "/Cache/GRCh38/Both" + String path_supplementary_annotations = "/SupplementaryAnnotation/GRCh38" + String path_reference = "/References/Homo_sapiens.GRCh38.Nirvana.dat" + + command <<< + set -e + + # NOTE: Validate a lil so that we don't waste time copying down the data sources if there's an error. + # ======================================= + # Handle our data sources: + + # Extract the tar.gz: + echo "Extracting annotation data sources tar/gzip file..." + mkdir datasources_dir + tar zxvf ~{nirvana_data_tar} -C datasources_dir --strip-components 2 + DATA_SOURCES_FOLDER="$PWD/datasources_dir" + + dotnet ~{nirvana_location} \ + -c $DATA_SOURCES_FOLDER~{path} \ + --sd $DATA_SOURCES_FOLDER~{path_supplementary_annotations} \ + -r $DATA_SOURCES_FOLDER~{path_reference} \ + -i ~{input_vcf} \ + -o ~{output_annotated_file_name} + >>> + # ------------------------------------------------ + # Runtime settings: + runtime { + docker: "annotation/nirvana:3.14" + memory: "3 GB" + cpu: "1" + disks: "local-disk 100 HDD" + } + # ------------------------------------------------ + # Outputs: + output { + File annotation_json = "~{annotation_json_name}" + File annotation_json_jsi = "~{annotation_json_name_jsi}" + } +} + From 7444ae6c76315f46e5a985dc44664e761932767e Mon Sep 17 00:00:00 2001 From: rori <6863459+RoriCremer@users.noreply.github.com> Date: Tue, 15 Jun 2021 22:11:53 -0400 Subject: [PATCH 07/73] update the schema --- hello_did_I_annotate_test.json | 299 ++++++++++++++ hello_did_I_annotate_testt.json | 299 ++++++++++++++ scripts/variantstore/wdl/NirvanaOutput.json | 10 + .../create_variant_annotation_table.py | 385 ++++++++++++++++++ .../variantstore/wdl/schemas/vat_schema.json | 194 ++++----- 5 files changed, 1096 insertions(+), 91 deletions(-) create mode 100644 hello_did_I_annotate_test.json create mode 100644 hello_did_I_annotate_testt.json create mode 100644 scripts/variantstore/wdl/NirvanaOutput.json create mode 100644 scripts/variantstore/wdl/extract/create_variant_annotation_table.py diff --git a/hello_did_I_annotate_test.json b/hello_did_I_annotate_test.json new file mode 100644 index 00000000000..13f2922e001 --- /dev/null +++ b/hello_did_I_annotate_test.json @@ -0,0 +1,299 @@ +{"header":{"annotator":"Nirvana 3.13.0","creationTime":"2021-06-12 01:47:58","genomeAssembly":"GRCh38","schemaVersion":6,"dataVersion":"91.27.61","dataSources":[{"name":"VEP","version":"91","description":"BothRefSeqAndEnsembl","releaseDate":"2017-12-18"},{"name":"MultiZ100Way","version":"20171006","description":"Amino acid conservation scores calculated from 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+{"chromosome":"chr20","position":199139,"refAllele":"C","altAlleles":["CTT"],"cytogeneticBand":"20p13","variants":[{"vid":"20-199139-C-CTT","chromosome":"chr20","begin":199140,"end":199139,"refAllele":"-","altAllele":"TT","variantType":"insertion","hgvsg":"NC_000020.11:g.199161_199162dupTT","inLowComplexityRegion":true,"dbsnp":["rs1160950757"],"topmed":{"allAf":0.279339,"allAn":125568,"allAc":35076,"allHc":2288,"failedFilter":true}}]} +],"genes":[ +{"name":"DEFB126","gnomAD":{"pLi":4.08e-1,"pRec":4.78e-1,"pNull":1.14e-1,"synZ":-7.40e-1,"misZ":-2.62e-1,"loeuf":1.68e0}}, +{"name":"DEFB127","gnomAD":{"pLi":4.05e-1,"pRec":4.79e-1,"pNull":1.16e-1,"synZ":-2.93e-1,"misZ":-1.48e-1,"loeuf":1.69e0}}, +{"name":"DEFB128","gnomAD":{"pLi":3.96e-1,"pRec":4.82e-1,"pNull":1.22e-1,"synZ":-1.87e0,"misZ":-8.54e-1,"loeuf":1.72e0}} +]} diff --git a/scripts/variantstore/wdl/NirvanaOutput.json b/scripts/variantstore/wdl/NirvanaOutput.json new file mode 100644 index 00000000000..85bb7e4f5f2 --- /dev/null +++ b/scripts/variantstore/wdl/NirvanaOutput.json @@ -0,0 +1,10 @@ +{ + "GvsSitesOnlyVCF.gvs_extract_cohort_filtered_vcfs": ["gs://broad-dsp-spec-ops/scratch/rcremer/Nirvana/Data/anvil_expected.vcf"], + "GvsSitesOnlyVCF.output_sites_only_file_name": "hello_did_I_sites_only", + "GvsSitesOnlyVCF.output_merged_file_name": "hello_did_I_merge", + "GvsSitesOnlyVCF.output_annotated_file_name": "hello_did_I_annotate", + "GvsSitesOnlyVCF.nirvana_data_directory": "gs://broad-dsp-spec-ops/scratch/rcremer/Nirvana/NirvanaData.tar.gz", + "GvsSitesOnlyVCF.project_id": "spec-ops-aou" +} +{"chromosome":"chr20","position":199123,"refAllele":"T","altAlleles":["C"],"cytogeneticBand":"20p13","variants":[{"vid":"20-199123-T-C","chromosome":"chr20","begin":199123,"end":199123,"refAllele":"T","altAllele":"C","variantType":"SNV","hgvsg":"NC_000020.11:g.199123T>C","phylopScore":0.2,"dbsnp":["rs1946670"],"globalAllele":{"globalMinorAllele":"C","globalMinorAlleleFrequency":0.3774},"gnomad":{"coverage":16,"allAf":0.323628,"allAn":27374,"allAc":8859,"allHc":1729,"afrAf":0.166829,"afrAn":8194,"afrAc":1367,"afrHc":116,"amrAf":0.357784,"amrAn":668,"amrAc":239,"amrHc":49,"easAf":0.487871,"easAn":1484,"easAc":724,"easHc":174,"finAf":0.362152,"finAn":2082,"finAc":754,"finHc":182,"nfeAf":0.388041,"nfeAn":13764,"nfeAc":5341,"nfeHc":1122,"asjAf":0.345324,"asjAn":278,"asjAc":96,"asjHc":18,"othAf":0.373894,"othAn":904,"othAc":338,"othHc":68,"maleAf":0.325566,"maleAn":15450,"maleAc":5030,"maleHc":980,"femaleAf":0.321117,"femaleAn":11924,"femaleAc":3829,"femaleHc":749,"controlsAllAf":0.328082,"controlsAllAn":8632,"controlsAllAc":2832},"oneKg":{"allAf":0.377396,"afrAf":0.155068,"amrAf":0.402017,"easAf":0.556548,"eurAf":0.387674,"sasAf":0.465235,"allAn":5008,"afrAn":1322,"amrAn":694,"easAn":1008,"eurAn":1006,"sasAn":978,"allAc":1890,"afrAc":205,"amrAc":279,"easAc":561,"eurAc":390,"sasAc":455},"topmed":{"allAf":0.33769,"allAn":125568,"allAc":42403,"allHc":7982}}]}, +{"chromosome":"chr20","position":199139,"refAllele":"C","altAlleles":["CTT"],"cytogeneticBand":"20p13","variants":[{"vid":"20-199139-C-CTT","chromosome":"chr20","begin":199140,"end":199139,"refAllele":"-","altAllele":"TT","variantType":"insertion","hgvsg":"NC_000020.11:g.199161_199162dupTT","inLowComplexityRegion":true,"dbsnp":["rs1160950757"],"topmed":{"allAf":0.279339,"allAn":125568,"allAc":35076,"allHc":2288,"failedFilter":true}}]} \ No newline at end of file diff --git a/scripts/variantstore/wdl/extract/create_variant_annotation_table.py b/scripts/variantstore/wdl/extract/create_variant_annotation_table.py new file mode 100644 index 00000000000..6b44c34a139 --- /dev/null +++ b/scripts/variantstore/wdl/extract/create_variant_annotation_table.py @@ -0,0 +1,385 @@ +# -*- coding: utf-8 -*- +import uuid +import time +import datetime + +from google.cloud import bigquery +from google.cloud.bigquery.job import QueryJobConfig +from google.oauth2 import service_account + +import argparse +import re + +JOB_IDS = set() + +# +# CONSTANTS +# +PET_TABLE_PREFIX = "pet_" +VET_TABLE_PREFIX = "vet_" +SAMPLES_PER_PARTITION = 4000 + +FINAL_TABLE_TTL = "" +#FINAL_TABLE_TTL = " OPTIONS( expiration_timestamp=TIMESTAMP_ADD(CURRENT_TIMESTAMP(), INTERVAL 72 HOUR)) " + +# temp-table-uuid +output_table_prefix = str(uuid.uuid4()).split("-")[0] +print(f"running with prefix {output_table_prefix}") + +PET_VET_TABLE_COUNT = -1 +client = None + +VET_DISTINCT_POS_TABLE = f"{output_table_prefix}_vet_distinct_pos" +PET_NEW_TABLE = f"{output_table_prefix}_pet_new" +VET_NEW_TABLE = f"{output_table_prefix}_vet_new" +EXTRACT_SAMPLE_TABLE = f"{output_table_prefix}_sample_names" + +def utf8len(s): + return len(s.encode('utf-8')) + +def dump_job_stats(): + total = 0 + + for jobid in JOB_IDS: + job = client.get_job(jobid[1]) + + bytes_billed = int(0 if job.total_bytes_billed is None else job.total_bytes_billed) + total = total + bytes_billed + + print(jobid[0], " <====> Cache Hit:", job.cache_hit, bytes_billed/(1024 * 1024), " MBs") + + print(" Total GBs billed ", total/(1024 * 1024 * 1024), " GBs") + +def execute_with_retry(label, sql): + retry_delay = [30, 60, 90] # 3 retries with incremental backoff + start = time.time() + while len(retry_delay) > 0: + try: + query_label = label.replace(" ","-").strip().lower() + + existing_labels = client._default_query_job_config.labels + job_labels = existing_labels + job_labels["gvs_query_name"] = query_label + job_config = bigquery.QueryJobConfig(labels=job_labels) + query = client.query(sql, job_config=job_config) + + print(f"STARTING - {label}") + JOB_IDS.add((label, query.job_id)) + results = query.result() + print(f"COMPLETED ({time.time() - start} s, {3-len(retry_delay)} retries) - {label}") + return results + except Exception as err: + # if there are no retries left... raise + if (len(retry_delay) == 0): + raise err + else: + t = retry_delay.pop(0) + print(f"Error {err} running query {label}, sleeping for {t}") + time.sleep(t) + +def get_partition_range(i): + if i < 1 or i > PET_VET_TABLE_COUNT: + raise ValueError(f"out of partition range") + + return { 'start': (i-1)*SAMPLES_PER_PARTITION + 1, 'end': i*SAMPLES_PER_PARTITION } + +def get_samples_for_partition(sample_ids, i): + return [ s for s in sample_ids if s >= get_partition_range(i)['start'] and s <= get_partition_range(i)['end'] ] + +def split_lists(samples, n): + return [samples[i * n:(i + 1) * n] for i in range((len(samples) + n - 1) // n )] + +def load_sample_names(sample_names_to_extract, fq_temp_table_dataset): + schema = [ bigquery.SchemaField("sample_name", "STRING", mode="REQUIRED") ] + fq_sample_table = f"{fq_temp_table_dataset}.{EXTRACT_SAMPLE_TABLE}" + + job_labels = client._default_query_job_config.labels + job_labels["gvs_query_name"] = "load-sample-names" + + job_config = bigquery.LoadJobConfig(source_format=bigquery.SourceFormat.CSV, skip_leading_rows=0, schema=schema, labels=job_labels) + + with open(sample_names_to_extract, "rb") as source_file: + job = client.load_table_from_file(source_file, fq_sample_table, job_config=job_config) + + job.result() # Waits for the job to complete. + + # setting the TTL needs to be done as a second API call + table = bigquery.Table(fq_sample_table, schema=schema) + expiration = datetime.datetime.utcnow() + datetime.timedelta(hours=TEMP_TABLE_TTL_HOURS) + table.expires = expiration + table = client.update_table(table, ["expires"]) + + return fq_sample_table + +def get_all_sample_ids(fq_destination_table_samples): + sql = f"select sample_id from `{fq_destination_table_samples}`" + + results = execute_with_retry("read cohort sample table", sql) + sample_ids = [row.sample_id for row in list(results)] + sample_ids.sort() + return sample_ids + +def create_extract_samples_table(fq_destination_table_samples, fq_sample_name_table, fq_sample_mapping_table): + sql = f"CREATE OR REPLACE TABLE `{fq_destination_table_samples}` AS (" \ + f"SELECT m.sample_id, m.sample_name FROM `{fq_sample_name_table}` s JOIN `{fq_sample_mapping_table}` m ON (s.sample_name = m.sample_name) )" + + results = execute_with_retry("create extract sample table", sql) + return results + +def get_table_count(fq_pet_vet_dataset): + sql = f"SELECT MAX(CAST(SPLIT(table_name, '_')[OFFSET(1)] AS INT64)) max_table_number " \ + f"FROM `{fq_pet_vet_dataset}.INFORMATION_SCHEMA.TABLES` " \ + f"WHERE REGEXP_CONTAINS(lower(table_name), r'^(pet_[0-9]+)$') " + results = execute_with_retry("get max table", sql) + return int([row.max_table_number for row in list(results)][0]) + +def make_new_vet_union_all(fq_pet_vet_dataset, fq_temp_table_dataset, sample_ids): + def get_subselect(fq_vet_table, samples, id): + sample_stanza = ','.join([str(s) for s in samples]) + sql = f" q_{id} AS (SELECT location, sample_id, ref, alt, call_GT, call_GQ, call_pl, QUALapprox, AS_QUALapprox from `{fq_vet_table}` WHERE sample_id IN ({sample_stanza})), " + return sql + + subs = {} + for i in range(1, PET_VET_TABLE_COUNT+1): + partition_samples = get_samples_for_partition(sample_ids, i) + + # KCIBUL -- grr, should be fixed width + fq_vet_table = f"{fq_pet_vet_dataset}.{VET_TABLE_PREFIX}{i:03}" + if len(partition_samples) > 0: + j = 1 + for samples in split_lists(partition_samples, 1000): + id = f"{i}_{j}" + subs[id] = get_subselect(fq_vet_table, samples, id) + j = j + 1 + + sql = f"create or replace table `{fq_temp_table_dataset}.{VET_NEW_TABLE}` {TEMP_TABLE_TTL} AS \n" + \ + "with\n" + \ + ("\n".join(subs.values())) + "\n" \ + "q_all AS (" + (" union all ".join([ f"(SELECT * FROM q_{id})" for id in subs.keys()])) + ")\n" + \ + f" (SELECT * FROM q_all)" + + print(sql) + print(f"VET Query is {utf8len(sql)/(1024*1024)} MB in length") + results = execute_with_retry("insert vet new table", sql) + return results + + + +def create_position_table(fq_temp_table_dataset, min_variant_samples): + dest = f"{fq_temp_table_dataset}.{VET_DISTINCT_POS_TABLE}" + + # only create this clause if min_variant_samples > 0, because if + # it is == 0 then we don't need to touch the sample_id column (which doubles the cost of this query) + min_sample_clause = "" + if min_variant_samples > 0: + min_sample_clause = f"HAVING count(distinct sample_id) >= {min_variant_samples}" + + sql = f""" + create or replace table `{dest}` {TEMP_TABLE_TTL} + as ( + select location from `{fq_temp_table_dataset}.{VET_NEW_TABLE}` WHERE alt != '*' GROUP BY location {min_sample_clause} + ) + """ + existing_labels = client._default_query_job_config.labels + job_labels = existing_labels + job_labels["gvs_query_name"] = "create-position-table" + job_config = bigquery.QueryJobConfig(labels=job_labels) + create_vet_distinct_pos_query = client.query(sql, job_config=job_config) + + create_vet_distinct_pos_query.result() + JOB_IDS.add((f"create positions table {dest}", create_vet_distinct_pos_query.job_id)) + return + +def make_new_pet_union_all(fq_pet_vet_dataset, fq_temp_table_dataset, sample_ids): + def get_pet_subselect(fq_pet_table, samples, id): + sample_stanza = ','.join([str(s) for s in samples]) + sql = f" q_{id} AS (SELECT p.location, p.sample_id, p.state from {fq_pet_table} p " \ + f" join `{fq_temp_table_dataset}.{VET_DISTINCT_POS_TABLE}` v on (p.location = v.location) WHERE p.sample_id IN ({sample_stanza})), " + return sql + + subs = {} + for i in range(1, PET_VET_TABLE_COUNT+1): + partition_samples = get_samples_for_partition(sample_ids, i) + + # KCIBUL -- grr, should be fixed width + fq_pet_table = f"{fq_pet_vet_dataset}.{PET_TABLE_PREFIX}{i:03}" + if len(partition_samples) > 0: + j = 1 + for samples in split_lists(partition_samples, 1000): + id = f"{i}_{j}" + subs[id] = get_pet_subselect(fq_pet_table, samples, id) + j = j + 1 + + sql = f"create or replace table `{fq_temp_table_dataset}.{PET_NEW_TABLE}` {TEMP_TABLE_TTL} AS \n" + \ + "with\n" + \ + ("\n".join(subs.values())) + "\n" \ + "q_all AS (" + (" union all ".join([ f"(SELECT * FROM q_{id})" for id in subs.keys()])) + ")\n" + \ + f" (SELECT * FROM q_all)" + + print(sql) + print(f"PET Query is {utf8len(sql)/(1024*1024)} MB in length") + results = execute_with_retry("insert pet new table", sql) + return results + + +def populate_final_extract_table(fq_temp_table_dataset, fq_destination_table_data, fq_sample_mapping_table): + sql = f""" + CREATE OR REPLACE TABLE `{fq_destination_table_data}` + PARTITION BY RANGE_BUCKET(location, GENERATE_ARRAY(0, 26000000000000, 6500000000)) + CLUSTER BY location + {FINAL_TABLE_TTL} + as (SELECT + new_pet.location, + s.sample_name as sample_name, + new_pet.state, + new_vet.ref, + REPLACE(new_vet.alt,",","") alt, + new_vet.call_GT, + new_vet.call_GQ, + cast(SPLIT(new_vet.call_pl,",")[OFFSET(0)] as int64) as call_RGQ, + new_vet.QUALapprox, + new_vet.AS_QUALapprox, + new_vet.call_PL + FROM + `{fq_temp_table_dataset}.{PET_NEW_TABLE}` new_pet + LEFT OUTER JOIN + `{fq_temp_table_dataset}.{VET_NEW_TABLE}` new_vet + ON (new_pet.location = new_vet.location AND new_pet.sample_id = new_vet.sample_id) + LEFT OUTER JOIN + `{fq_sample_mapping_table}` s ON (new_pet.sample_id = s.sample_id)) + """ + print(sql) + existing_labels = client._default_query_job_config.labels + job_labels = existing_labels + job_labels["gvs_query_name"] = "populate-final-extract-table" + job_config = bigquery.QueryJobConfig(labels=job_labels) + cohort_extract_final_query_job = client.query(sql, job_config=job_config) + + cohort_extract_final_query_job.result() + JOB_IDS.add((f"insert final cohort table {fq_destination_table_data}", cohort_extract_final_query_job.job_id)) + return + +def make_extract_table(fq_pet_vet_dataset, + max_tables, + sample_names_to_extract, + fq_cohort_sample_names, + query_project, + query_labels, + fq_temp_table_dataset, + fq_destination_dataset, + destination_table_prefix, + min_variant_samples, + fq_sample_mapping_table, + sa_key_path, + temp_table_ttl_hours + ): + try: + fq_destination_table_data = f"{fq_destination_dataset}.{destination_table_prefix}__DATA" + fq_destination_table_samples = f"{fq_destination_dataset}.{destination_table_prefix}__SAMPLES" + + global client + # this is where a set of labels are being created for the cohort extract + query_labels_map = {} + query_labels_map["id"]= output_table_prefix + query_labels_map["gvs_tool_name"]= "gvs_prepare_callset" + + # query_labels is string that looks like 'key1=val1, key2=val2' + if query_labels is not None and len(query_labels) != 0: + for query_label in query_labels: + kv = query_label.split("=", 2) + key = kv[0].strip().lower() + value = kv[1].strip().lower() + query_labels_map[key] = value + + if not (bool(re.match(r"[a-z0-9_-]+$", key)) & bool(re.match(r"[a-z0-9_-]+$", value))): + raise ValueError(f"label key or value did not pass validation--format should be 'key1=val1, key2=val2'") + + #Default QueryJobConfig will be merged into job configs passed in + #but if a specific default config is being updated (eg labels), new config must be added + #to the client._default_query_job_config that already exists + default_config = QueryJobConfig(labels=query_labels_map, priority="INTERACTIVE", use_query_cache=False) + + if sa_key_path: + credentials = service_account.Credentials.from_service_account_file( + sa_key_path, scopes=["https://www.googleapis.com/auth/cloud-platform"], + ) + + client = bigquery.Client(credentials=credentials, + project=query_project, + default_query_job_config=default_config) + else: + client = bigquery.Client(project=query_project, + default_query_job_config=default_config) + + ## TODO -- provide a cmdline arg to override this (so we can simulate smaller datasets) + + global PET_VET_TABLE_COUNT + PET_VET_TABLE_COUNT = max_tables + + global TEMP_TABLE_TTL_HOURS + TEMP_TABLE_TTL_HOURS = temp_table_ttl_hours + + global TEMP_TABLE_TTL + TEMP_TABLE_TTL = f" OPTIONS( expiration_timestamp=TIMESTAMP_ADD(CURRENT_TIMESTAMP(), INTERVAL {TEMP_TABLE_TTL_HOURS} HOUR)) " + + print(f"Using {PET_VET_TABLE_COUNT} PET tables in {fq_pet_vet_dataset}...") + + # if we have a file of sample names, load it into a temporary table + if (sample_names_to_extract): + fq_sample_name_table = load_sample_names(sample_names_to_extract, fq_temp_table_dataset) + else: + fq_sample_name_table = fq_cohort_sample_names + + # At this point one way or the other we have a table of sample names in BQ, + # join it to the sample_info table to drive the extract + create_extract_samples_table(fq_destination_table_samples, fq_sample_name_table, fq_sample_mapping_table) + + # pull the sample ids back down + sample_ids = get_all_sample_ids(fq_destination_table_samples) + print(f"Discovered {len(sample_ids)} samples in {fq_destination_table_samples}...") + + make_new_vet_union_all(fq_pet_vet_dataset, fq_temp_table_dataset, sample_ids) + + create_position_table(fq_temp_table_dataset, min_variant_samples) + make_new_pet_union_all(fq_pet_vet_dataset, fq_temp_table_dataset, sample_ids) + populate_final_extract_table(fq_temp_table_dataset, fq_destination_table_data, fq_destination_table_samples) + finally: + dump_job_stats() + + print(f"\nFinal cohort extract data written to {fq_destination_table_data}\n") + +if __name__ == '__main__': + parser = argparse.ArgumentParser(allow_abbrev=False, description='Extract a cohort from BigQuery Variant Store ') + + parser.add_argument('--fq_petvet_dataset',type=str, help='project.dataset location of pet/vet data', required=True) + parser.add_argument('--fq_temp_table_dataset',type=str, help='project.dataset location where results should be stored', required=True) + parser.add_argument('--fq_destination_dataset',type=str, help='project.dataset location where results should be stored', required=True) + parser.add_argument('--destination_cohort_table_prefix',type=str, help='prefix used for destination cohort extract tables (e.g. my_fantastic_cohort)', required=True) + parser.add_argument('--query_project',type=str, help='Google project where query should be executed', required=True) + parser.add_argument('--query_labels',type=str, action='append', help='Labels to put on the BQ query that will show up in the billing. Ex: --query_labels key1=value1 --query_labels key2=value2', required=False) + parser.add_argument('--min_variant_samples',type=int, help='Minimum variant samples at a site required to be emitted', required=False, default=0) + parser.add_argument('--fq_sample_mapping_table',type=str, help='Mapping table from sample_id to sample_name', required=True) + parser.add_argument('--sa_key_path',type=str, help='Path to json key file for SA', required=False) + parser.add_argument('--max_tables',type=int, help='Maximum number of PET/VET tables to consider', required=False, default=250) + parser.add_argument('--ttl',type=int, help='Temp table TTL in hours', required=False, default=72) + sample_args = parser.add_mutually_exclusive_group(required=True) + sample_args.add_argument('--sample_names_to_extract',type=str, help='File containing list of samples to extract, 1 per line') + sample_args.add_argument('--fq_cohort_sample_names',type=str, help='FQN of cohort table to extract, contains "sample_name" column') + + + # Execute the parse_args() method + args = parser.parse_args() + + make_extract_table(args.fq_petvet_dataset, + args.max_tables, + args.sample_names_to_extract, + args.fq_cohort_sample_names, + args.query_project, + args.query_labels, + args.fq_temp_table_dataset, + args.fq_destination_dataset, + args.destination_cohort_table_prefix, + args.min_variant_samples, + args.fq_sample_mapping_table, + args.sa_key_path, + args.ttl) diff --git a/scripts/variantstore/wdl/schemas/vat_schema.json b/scripts/variantstore/wdl/schemas/vat_schema.json index 42935ea18a6..38eea23fa57 100644 --- a/scripts/variantstore/wdl/schemas/vat_schema.json +++ b/scripts/variantstore/wdl/schemas/vat_schema.json @@ -1,41 +1,59 @@ [ + { + "description": "Must be positive. Exact position for a SNP and the position before the alteration in an indel", + "name": "position", + "type": "Integer", + "mode": "Required" + }, { "description": "Variant ID. Unique string for identifying a variant (as produced by NIRVANA based on a spec from Broad Institute)", "name": "vid", "type": "String", "mode": "Required" }, - { - "description": "Transcript ID. Null indicates that this variant does not overlap any transcripts", - "name": "transcript", - "type": "String", - "mode": "Nullable" - }, { "description": "Contig names match the hg38 reference", "name": "contig", "type": "String", - "mode": "Nullable" - }, -{ - "description": "Must be positive. Exact position for a SNP and the position before the alteration in an indel", - "name": "position", - "type": "Integer", "mode": "Required" }, { "description": "base(s). This should always be one base for SNPs and insertions. More than one base for deletions", "name": "ref_allele", "type": "String", - "mode": "Nullable" + "mode": "Required" }, { "description": "base(s). This should always be one base for SNPs and deletions. More than one base for insertions", "name": "alt_allele", "type": "String", - "mode": "Nullable" + "mode": "Required" }, { + "description": "DNA change type (HGVS)", + "name": "variant_type", + "type": "String", + "mode": "Required" + }, + { + "description": "HGVS g. nomenclature Variant location", + "name": "genomic_location", + "type": "String", + "mode": "Required" + }, + { + "description": "rsID", + "name": "dbsnp_rsid", + "type": "String", + "mode": "Nullable" + }, + { + "description": "Transcript ID. Null indicates that this variant does not overlap any transcripts", + "name": "transcript", + "type": "String", + "mode": "Nullable" + }, + { "description": "Gene symbol. A variant can have more than one associated gene symbol, since about 3% of genes do overlap", "name": "gene_symbol", "type": "String", @@ -43,7 +61,7 @@ }, { "description": "", - "name": "transcript _source", + "name": "transcript_source", "type": "String", "mode": "Nullable" }, @@ -64,12 +82,6 @@ "name": "dna_change", "type": "String", "mode": "Nullable" - }, - { - "description": "DNA change type (HGVS)", - "name": "variant_type", - "type": "String", - "mode": "Nullable" }, { "description": "Exon number", @@ -83,42 +95,18 @@ "type": "String", "mode": "Nullable" }, - { - "description": "HGVS g. nomenclature Variant location", - "name": "genomic_location", - "type": "String", - "mode": "Nullable" - }, { "description": "Splice site distance for introns Will be a positive or negative integer", "name": "splice_distance", "type": "String", "mode": "Nullable" }, - { - "description": "rsID", - "name": "dbsnp_rsid", - "type": "String", - "mode": "Nullable" - }, { "description": "Entrez/NCBI ID", "name": "entrez_gene_id", "type": "String", "mode": "Nullable" }, - { - "description": "HGNC ID", - "name": "hgnc_gene_id", - "type": "String", - "mode": "Nullable" - }, - { - "description": "OMIM ID", - "name": "gene_omim_id", - "type": "Integer", - "mode": "Nullable" - }, { "description": "Primary Transcript ID", "name": "is_canonical_transcript", @@ -126,47 +114,23 @@ "mode": "Nullable" }, { - "description": "gnomAD: 'Total' frequency", - "name": "gnomad_all_af", - "type": "Float", - "mode": "Nullable" - }, - { - "description": "gnomAD: 'Total' allele count", - "name": "gnomad_all_ac", - "type": "Integer", + "description": "AC TODO -- this needs to be added back and swapped to required", + "name": "gvs_all_ac", + "type": "String", "mode": "Nullable" }, { - "description": "gnomAD: 'Total' allele number", - "name": "gnomad_all_an", + "description": "AN TODO -- this needs to be added back and swapped to required", + "name": "gvs_all_an", "type": "Integer", "mode": "Nullable" }, { - "description": "gnomAD: Max subpopulation frequency", - "name": "gnomad_max_af", + "description": "AF TODO -- this needs to be added back and swapped to required", + "name": "gvs_all_af", "type": "Float", "mode": "Nullable" }, - { - "description": "gnomAD: Max subpopulation count", - "name": "gnomad_max_ac", - "type": "Integer", - "mode": "Nullable" - }, - { - "description": "gnomAD: Max subpopulation number", - "name": "gnomad_max_an", - "type": "Integer", - "mode": "Nullable" - }, - { - "description": "gnomAD: Max subpopulation ethnicity", - "name": "gnomad_max_subpop", - "type": "String", - "mode": "Nullable" - }, { "description": "REVEL", "name": "revel", @@ -221,18 +185,6 @@ "type": "Integer", "mode": "Nullable" }, - { - "description": "OMIM Disease ID", - "name": "omim_phenotypes_id", - "type": "Integer", - "mode": "Repeated" - }, - { - "description": "OMIM Disease Name", - "name": "omim_phenotypes_name", - "type": "String", - "mode": "Repeated" - }, { "description": "ClinVar Classification", "name": "clinvar_classification", @@ -246,9 +198,69 @@ "mode": "Nullable" }, { - "description": "ClinVar Disease Name", + "description": "ClinVar Disease Name TODO -- this needs to be swapped to Repeated not nullable", "name": "clinvar_phenotype", "type": "String", - "mode": "Repeated" - } + "mode": "Nullable" + }, + { + "description": "gnomAD: 'Total' frequency", + "name": "gnomad_all_af", + "type": "Float", + "mode": "Nullable" + }, + { + "description": "gnomAD: 'Total' allele count", + "name": "gnomad_all_ac", + "type": "Integer", + "mode": "Nullable" + }, + { + "description": "gnomAD: 'Total' allele number", + "name": "gnomad_all_an", + "type": "Integer", + "mode": "Nullable" + }, + { + "description": "gnomAD: Max subpopulation frequency", + "name": "gnomad_max_af", + "type": "Float", + "mode": "Nullable" + }, + { + "description": "gnomAD: Max subpopulation count", + "name": "gnomad_max_ac", + "type": "Integer", + "mode": "Nullable" + }, + { + "description": "gnomAD: Max subpopulation number", + "name": "gnomad_max_an", + "type": "Integer", + "mode": "Nullable" + }, + { + "description": "gnomAD: Max subpopulation ethnicity", + "name": "gnomad_max_subpop", + "type": "String", + "mode": "Nullable" + }, + { + "description": "OMIM ID", + "name": "gene_omim_id", + "type": "Integer", + "mode": "Nullable" + }, + { + "description": "OMIM Disease ID TODO -- this needs to be swapped to Repeated not nullable", + "name": "omim_phenotypes_id", + "type": "Integer", + "mode": "Nullable" + }, + { + "description": "OMIM Disease Name TODO -- this needs to be swapped to Repeated not nullable", + "name": "omim_phenotypes_name", + "type": "String", + "mode": "Nullable" + } ] From 11766e1f59a638e15d207d1ef15888b07b5d1b46 Mon Sep 17 00:00:00 2001 From: rori <6863459+RoriCremer@users.noreply.github.com> Date: Tue, 15 Jun 2021 22:15:29 -0400 Subject: [PATCH 08/73] clean up test files --- hello_did_I_annotate_test.json | 299 -------------------- scripts/variantstore/wdl/NirvanaOutput.json | 10 - 2 files changed, 309 deletions(-) delete mode 100644 hello_did_I_annotate_test.json delete mode 100644 scripts/variantstore/wdl/NirvanaOutput.json diff --git a/hello_did_I_annotate_test.json b/hello_did_I_annotate_test.json deleted file mode 100644 index 13f2922e001..00000000000 --- a/hello_did_I_annotate_test.json +++ /dev/null @@ -1,299 +0,0 @@ -{"header":{"annotator":"Nirvana 3.13.0","creationTime":"2021-06-12 01:47:58","genomeAssembly":"GRCh38","schemaVersion":6,"dataVersion":"91.27.61","dataSources":[{"name":"VEP","version":"91","description":"BothRefSeqAndEnsembl","releaseDate":"2017-12-18"},{"name":"MultiZ100Way","version":"20171006","description":"Amino acid conservation scores calculated from MultiZ100Way alignments from UCSC.","releaseDate":"2017-10-06"},{"name":"ClinVar","version":"20200903","description":"A freely accessible, public archive of reports of the relationships among human variations and phenotypes, with supporting evidence","releaseDate":"2020-09-03"},{"name":"dbSNP","version":"154","description":"Identifiers for observed variants","releaseDate":"2020-05-01"},{"name":"dbSNP","version":"151","description":"Identifiers for observed variants","releaseDate":"2018-04-18"},{"name":"gnomAD","version":"2.1","description":"gnomAD allele frequency data remapped to GRCh38 with CrossMap by Ensembl","releaseDate":"2019-03-25"},{"name":"MITOMAP","version":"20200819","description":"Small variants in the MITOMAP human mitochondrial genome database","releaseDate":"2020-08-19"},{"name":"1000 Genomes Project","version":"Phase 3 v3plus","description":"A public catalogue of human variation and genotype data","releaseDate":"2013-05-27"},{"name":"PrimateAI","version":"0.2","description":"PrimateAI percentile scores.","releaseDate":"2018-11-07"},{"name":"REVEL","version":"20200205","description":"Pathogenicity scores of missense variants predicted by REVEL","releaseDate":"2020-02-05"},{"name":"SpliceAI","version":"1.3","description":"SpliceAI scores, distances, etc.","releaseDate":"2019-10-04"},{"name":"TOPMed","version":"freeze_5","description":"Allele frequencies from TOPMed data","releaseDate":"2017-08-28"},{"name":"ClinGen","version":"20160414","releaseDate":"2016-04-14"},{"name":"ClinGen Dosage Sensitivity Map","version":"20200913","description":"Dosage sensitivity map from ClinGen (dbVar)","releaseDate":"2020-09-13"},{"name":"MITOMAP_SV","version":"20200819","description":"Large structural variants in the MITOMAP human mitochondrial genome database","releaseDate":"2020-08-19"},{"name":"1000 Genomes Project (SV)","version":"Phase 3 v5a","description":"A public catalogue of human variation and genotype data","releaseDate":"2013-05-27"},{"name":"ClinGen disease validity curations","version":"20200914","description":"Disease validity curations from ClinGen (dbVar)","releaseDate":"2020-09-14"},{"name":"gnomAD_gene_scores","version":"2.1","description":"Gene Loss of function scores from Genome Aggregation Database (gnomAD)","releaseDate":"2018-10-17"},{"name":"OMIM","version":"20200915","description":"An Online Catalog of Human Genes and Genetic Disorders","releaseDate":"2020-09-15"},{"name":"phyloP","version":"hg38","description":"20 way conservation score between humans and 19 other vertebrates","releaseDate":"2015-04-17"},{"name":"gnomAD_LCR","version":"2.1","description":"Low complexity regions from gnomAD.","releaseDate":"2019-04-10"},{"name":"MitochondrialHeteroplasmy","version":"20180410","description":"Variant read frequency percentiles for the Mitochondrial reference","releaseDate":"2020-05-21"}]},"positions":[ 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-{"chromosome":"chr20","position":198921,"refAllele":"A","altAlleles":["G"],"cytogeneticBand":"20p13","variants":[{"vid":"20-198921-A-G","chromosome":"chr20","begin":198921,"end":198921,"refAllele":"A","altAllele":"G","variantType":"SNV","hgvsg":"NC_000020.11:g.198921A>G","phylopScore":-2.1,"dbsnp":["rs6033277"],"globalAllele":{"globalMinorAllele":"A","globalMinorAlleleFrequency":0.4696},"gnomad":{"coverage":19,"allAf":0.508515,"allAn":31240,"allAc":15886,"allHc":3999,"afrAf":0.511427,"afrAn":8664,"afrAc":4431,"afrHc":1080,"amrAf":0.477435,"amrAn":842,"amrAc":402,"amrHc":96,"easAf":0.500645,"easAn":1550,"easAc":776,"easHc":191,"finAf":0.494804,"finAn":3464,"finAc":1714,"finHc":439,"nfeAf":0.513748,"nfeAn":15348,"nfeAc":7885,"nfeHc":2027,"asjAf":0.47931,"asjAn":290,"asjAc":139,"asjHc":31,"othAf":0.498152,"othAn":1082,"othAc":539,"othHc":135,"maleAf":0.508913,"maleAn":17390,"maleAc":8850,"maleHc":2200,"femaleAf":0.508014,"femaleAn":13850,"femaleAc":7036,"femaleHc":1799,"controlsAllAf":0.510287,"controlsAllAn":10790,"controlsAllAc":5506},"oneKg":{"allAf":0.530351,"afrAf":0.520424,"amrAf":0.482709,"easAf":0.566468,"eurAf":0.478131,"sasAf":0.59407,"allAn":5008,"afrAn":1322,"amrAn":694,"easAn":1008,"eurAn":1006,"sasAn":978,"allAc":2656,"afrAc":688,"amrAc":335,"easAc":571,"eurAc":481,"sasAc":581},"topmed":{"allAf":0.507725,"allAn":125568,"allAc":63754,"allHc":16184}}]}, -{"chromosome":"chr20","position":199094,"refAllele":"TTAAAA","altAlleles":["T"],"cytogeneticBand":"20p13","variants":[{"vid":"20-199094-TTAAAA-T","chromosome":"chr20","begin":199095,"end":199099,"refAllele":"TAAAA","altAllele":"-","variantType":"deletion","hgvsg":"NC_000020.11:g.199100_199104del","dbsnp":["rs76051089"],"gnomad":{"coverage":17,"allAf":0.143474,"allAn":28932,"allAc":4151,"allHc":385,"afrAf":0.05794,"afrAn":8388,"afrAc":486,"afrHc":12,"amrAf":0.127005,"amrAn":748,"amrAc":95,"amrHc":8,"easAf":0.085286,"easAn":1536,"easAc":131,"easHc":4,"finAf":0.169538,"finAn":2554,"finAc":433,"finHc":47,"nfeAf":0.193446,"nfeAn":14464,"nfeAc":2798,"nfeHc":296,"asjAf":0.163121,"asjAn":282,"asjAc":46,"asjHc":4,"othAf":0.16875,"othAn":960,"othAc":162,"othHc":14,"maleAf":0.143412,"maleAn":16212,"maleAc":2325,"maleHc":212,"femaleAf":0.143553,"femaleAn":12720,"femaleAc":1826,"femaleHc":173,"controlsAllAf":0.137913,"controlsAllAn":9448,"controlsAllAc":1303},"oneKg":{"allAf":0.096446,"afrAf":0.024206,"amrAf":0.123919,"easAf":0.064484,"eurAf":0.229622,"sasAf":0.070552,"allAn":5008,"afrAn":1322,"amrAn":694,"easAn":1008,"eurAn":1006,"sasAn":978,"allAc":483,"afrAc":32,"amrAc":86,"easAc":65,"eurAc":231,"sasAc":69},"topmed":{"allAf":0.148398,"allAn":125568,"allAc":18634,"allHc":1612,"failedFilter":true}}]}, -{"chromosome":"chr20","position":199123,"refAllele":"T","altAlleles":["C"],"cytogeneticBand":"20p13","variants":[{"vid":"20-199123-T-C","chromosome":"chr20","begin":199123,"end":199123,"refAllele":"T","altAllele":"C","variantType":"SNV","hgvsg":"NC_000020.11:g.199123T>C","phylopScore":0.2,"dbsnp":["rs1946670"],"globalAllele":{"globalMinorAllele":"C","globalMinorAlleleFrequency":0.3774},"gnomad":{"coverage":16,"allAf":0.323628,"allAn":27374,"allAc":8859,"allHc":1729,"afrAf":0.166829,"afrAn":8194,"afrAc":1367,"afrHc":116,"amrAf":0.357784,"amrAn":668,"amrAc":239,"amrHc":49,"easAf":0.487871,"easAn":1484,"easAc":724,"easHc":174,"finAf":0.362152,"finAn":2082,"finAc":754,"finHc":182,"nfeAf":0.388041,"nfeAn":13764,"nfeAc":5341,"nfeHc":1122,"asjAf":0.345324,"asjAn":278,"asjAc":96,"asjHc":18,"othAf":0.373894,"othAn":904,"othAc":338,"othHc":68,"maleAf":0.325566,"maleAn":15450,"maleAc":5030,"maleHc":980,"femaleAf":0.321117,"femaleAn":11924,"femaleAc":3829,"femaleHc":749,"controlsAllAf":0.328082,"controlsAllAn":8632,"controlsAllAc":2832},"oneKg":{"allAf":0.377396,"afrAf":0.155068,"amrAf":0.402017,"easAf":0.556548,"eurAf":0.387674,"sasAf":0.465235,"allAn":5008,"afrAn":1322,"amrAn":694,"easAn":1008,"eurAn":1006,"sasAn":978,"allAc":1890,"afrAc":205,"amrAc":279,"easAc":561,"eurAc":390,"sasAc":455},"topmed":{"allAf":0.33769,"allAn":125568,"allAc":42403,"allHc":7982}}]}, -{"chromosome":"chr20","position":199139,"refAllele":"C","altAlleles":["CTT"],"cytogeneticBand":"20p13","variants":[{"vid":"20-199139-C-CTT","chromosome":"chr20","begin":199140,"end":199139,"refAllele":"-","altAllele":"TT","variantType":"insertion","hgvsg":"NC_000020.11:g.199161_199162dupTT","inLowComplexityRegion":true,"dbsnp":["rs1160950757"],"topmed":{"allAf":0.279339,"allAn":125568,"allAc":35076,"allHc":2288,"failedFilter":true}}]} -],"genes":[ -{"name":"DEFB126","gnomAD":{"pLi":4.08e-1,"pRec":4.78e-1,"pNull":1.14e-1,"synZ":-7.40e-1,"misZ":-2.62e-1,"loeuf":1.68e0}}, -{"name":"DEFB127","gnomAD":{"pLi":4.05e-1,"pRec":4.79e-1,"pNull":1.16e-1,"synZ":-2.93e-1,"misZ":-1.48e-1,"loeuf":1.69e0}}, -{"name":"DEFB128","gnomAD":{"pLi":3.96e-1,"pRec":4.82e-1,"pNull":1.22e-1,"synZ":-1.87e0,"misZ":-8.54e-1,"loeuf":1.72e0}} -]} diff --git a/scripts/variantstore/wdl/NirvanaOutput.json b/scripts/variantstore/wdl/NirvanaOutput.json deleted file mode 100644 index 85bb7e4f5f2..00000000000 --- a/scripts/variantstore/wdl/NirvanaOutput.json +++ /dev/null @@ -1,10 +0,0 @@ -{ - "GvsSitesOnlyVCF.gvs_extract_cohort_filtered_vcfs": ["gs://broad-dsp-spec-ops/scratch/rcremer/Nirvana/Data/anvil_expected.vcf"], - "GvsSitesOnlyVCF.output_sites_only_file_name": "hello_did_I_sites_only", - "GvsSitesOnlyVCF.output_merged_file_name": "hello_did_I_merge", - "GvsSitesOnlyVCF.output_annotated_file_name": "hello_did_I_annotate", - "GvsSitesOnlyVCF.nirvana_data_directory": "gs://broad-dsp-spec-ops/scratch/rcremer/Nirvana/NirvanaData.tar.gz", - "GvsSitesOnlyVCF.project_id": "spec-ops-aou" -} -{"chromosome":"chr20","position":199123,"refAllele":"T","altAlleles":["C"],"cytogeneticBand":"20p13","variants":[{"vid":"20-199123-T-C","chromosome":"chr20","begin":199123,"end":199123,"refAllele":"T","altAllele":"C","variantType":"SNV","hgvsg":"NC_000020.11:g.199123T>C","phylopScore":0.2,"dbsnp":["rs1946670"],"globalAllele":{"globalMinorAllele":"C","globalMinorAlleleFrequency":0.3774},"gnomad":{"coverage":16,"allAf":0.323628,"allAn":27374,"allAc":8859,"allHc":1729,"afrAf":0.166829,"afrAn":8194,"afrAc":1367,"afrHc":116,"amrAf":0.357784,"amrAn":668,"amrAc":239,"amrHc":49,"easAf":0.487871,"easAn":1484,"easAc":724,"easHc":174,"finAf":0.362152,"finAn":2082,"finAc":754,"finHc":182,"nfeAf":0.388041,"nfeAn":13764,"nfeAc":5341,"nfeHc":1122,"asjAf":0.345324,"asjAn":278,"asjAc":96,"asjHc":18,"othAf":0.373894,"othAn":904,"othAc":338,"othHc":68,"maleAf":0.325566,"maleAn":15450,"maleAc":5030,"maleHc":980,"femaleAf":0.321117,"femaleAn":11924,"femaleAc":3829,"femaleHc":749,"controlsAllAf":0.328082,"controlsAllAn":8632,"controlsAllAc":2832},"oneKg":{"allAf":0.377396,"afrAf":0.155068,"amrAf":0.402017,"easAf":0.556548,"eurAf":0.387674,"sasAf":0.465235,"allAn":5008,"afrAn":1322,"amrAn":694,"easAn":1008,"eurAn":1006,"sasAn":978,"allAc":1890,"afrAc":205,"amrAc":279,"easAc":561,"eurAc":390,"sasAc":455},"topmed":{"allAf":0.33769,"allAn":125568,"allAc":42403,"allHc":7982}}]}, -{"chromosome":"chr20","position":199139,"refAllele":"C","altAlleles":["CTT"],"cytogeneticBand":"20p13","variants":[{"vid":"20-199139-C-CTT","chromosome":"chr20","begin":199140,"end":199139,"refAllele":"-","altAllele":"TT","variantType":"insertion","hgvsg":"NC_000020.11:g.199161_199162dupTT","inLowComplexityRegion":true,"dbsnp":["rs1160950757"],"topmed":{"allAf":0.279339,"allAn":125568,"allAc":35076,"allHc":2288,"failedFilter":true}}]} \ No newline at end of file From fd9b3ceceaabafce185b33ae6b153eb8bba6c036 Mon Sep 17 00:00:00 2001 From: rori <6863459+RoriCremer@users.noreply.github.com> Date: Tue, 15 Jun 2021 22:16:02 -0400 Subject: [PATCH 09/73] add project id to inputs --- scripts/variantstore/wdl/GvsSitesOnlyVCF.example.inputs.json | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/scripts/variantstore/wdl/GvsSitesOnlyVCF.example.inputs.json b/scripts/variantstore/wdl/GvsSitesOnlyVCF.example.inputs.json index c209b93c4d4..1f717674da7 100644 --- a/scripts/variantstore/wdl/GvsSitesOnlyVCF.example.inputs.json +++ b/scripts/variantstore/wdl/GvsSitesOnlyVCF.example.inputs.json @@ -3,5 +3,6 @@ "GvsSitesOnlyVCF.output_sites_only_file_name": "hello_did_I_sites_only", "GvsSitesOnlyVCF.output_merged_file_name": "hello_did_I_merge", "GvsSitesOnlyVCF.output_annotated_file_name": "hello_did_I_annotate", - "GvsSitesOnlyVCF.nirvana_data_directory": "gs://broad-dsp-spec-ops/scratch/rcremer/Nirvana/NirvanaData.tar.gz" + "GvsSitesOnlyVCF.nirvana_data_directory": "gs://broad-dsp-spec-ops/scratch/rcremer/Nirvana/NirvanaData.tar.gz", + "GvsSitesOnlyVCF.project_id": "spec-ops-aou" } From c3c46a6a66c3faf92b9c19e3f17608d1cb9466c8 Mon Sep 17 00:00:00 2001 From: rori <6863459+RoriCremer@users.noreply.github.com> Date: Wed, 16 Jun 2021 01:32:53 -0400 Subject: [PATCH 10/73] add jq and query --- scripts/variantstore/wdl/GvsSitesOnlyVCF.wdl | 387 +++++++++++++++++++ 1 file changed, 387 insertions(+) diff --git a/scripts/variantstore/wdl/GvsSitesOnlyVCF.wdl b/scripts/variantstore/wdl/GvsSitesOnlyVCF.wdl index 671072c9e5c..5fcdc7d8866 100644 --- a/scripts/variantstore/wdl/GvsSitesOnlyVCF.wdl +++ b/scripts/variantstore/wdl/GvsSitesOnlyVCF.wdl @@ -5,7 +5,275 @@ workflow GvsSitesOnlyVCF { String output_sites_only_file_name String output_merged_file_name String output_annotated_file_name + String project_id File nirvana_data_directory + String nirvana_schema = '[ + { + "description": "Must be positive. Exact position for a SNP and the position before the alteration in an indel", + "name": "position", + "type": "Integer", + "mode": "Required" + }, + { + "description": "Variant ID. Unique string for identifying a variant (as produced by NIRVANA based on a spec from Broad Institute)", + "name": "vid", + "type": "String", + "mode": "Required" + }, + { + "description": "Contig names match the hg38 reference", + "name": "contig", + "type": "String", + "mode": "Required" + }, + { + "description": "base(s). This should always be one base for SNPs and insertions. More than one base for deletions", + "name": "ref_allele", + "type": "String", + "mode": "Required" + }, + { + "description": "base(s). This should always be one base for SNPs and deletions. More than one base for insertions", + "name": "alt_allele", + "type": "String", + "mode": "Required" + }, + { + "description": "DNA change type (HGVS)", + "name": "variant_type", + "type": "String", + "mode": "Required" + }, + { + "description": "HGVS g. nomenclature Variant location", + "name": "genomic_location", + "type": "String", + "mode": "Required" + }, + { + "description": "rsID", + "name": "dbsnp_rsid", + "type": "String", + "mode": "Nullable" + }, + { + "description": "Transcript ID. Null indicates that this variant does not overlap any transcripts", + "name": "transcript", + "type": "String", + "mode": "Nullable" + }, + { + "description": "Gene symbol. A variant can have more than one associated gene symbol, since about 3% of genes do overlap", + "name": "gene_symbol", + "type": "String", + "mode": "Nullable" + }, + { + "description": "", + "name": "transcript_source", + "type": "String", + "mode": "Nullable" + }, + { + "description": "HGVS p. nomenclature; Amino acid change", + "name": "aa_change", + "type": "String", + "mode": "Nullable" + }, + { + "description": "Amino acid change type", + "name": "consequence", + "type": "String", + "mode": "Nullable" + }, + { + "description": "HGVS c. nomenclature; DNA change", + "name": "dna_change", + "type": "String", + "mode": "Nullable" + }, + { + "description": "Exon number", + "name": "exon_number", + "type": "String", + "mode": "Nullable" + }, + { + "description": "Intron number", + "name": "intron_number", + "type": "String", + "mode": "Nullable" + }, + { + "description": "Splice site distance for introns Will be a positive or negative integer", + "name": "splice_distance", + "type": "String", + "mode": "Nullable" + }, + { + "description": "Entrez/NCBI ID", + "name": "entrez_gene_id", + "type": "String", + "mode": "Nullable" + }, + { + "description": "Primary Transcript ID", + "name": "is_canonical_transcript", + "type": "String", + "mode": "Nullable" + }, + { + "description": "AC TODO -- this needs to be added back and swapped to required", + "name": "gvs_all_ac", + "type": "String", + "mode": "Nullable" + }, + { + "description": "AN TODO -- this needs to be added back and swapped to required", + "name": "gvs_all_an", + "type": "Integer", + "mode": "Nullable" + }, + { + "description": "AF TODO -- this needs to be added back and swapped to required", + "name": "gvs_all_af", + "type": "Float", + "mode": "Nullable" + }, + { + "description": "REVEL", + "name": "revel", + "type": "String", + "mode": "Nullable" + }, + { + "description": "Slice AI", + "name": "splice_ai_acceptor_gain_score", + "type": "Float", + "mode": "Nullable" + }, + { + "description": "Slice AI", + "name": "splice_ai_acceptor_gain_distance", + "type": "Integer", + "mode": "Nullable" + }, + { + "description": "Slice AI", + "name": "splice_ai_acceptor_loss_score", + "type": "Float", + "mode": "Nullable" + }, + { + "description": "Slice AI", + "name": "splice_ai_acceptor_loss_distance", + "type": "Integer", + "mode": "Nullable" + }, + { + "description": "Slice AI", + "name": "splice_ai_donor_gain_score", + "type": "Float", + "mode": "Nullable" + }, + { + "description": "Slice AI", + "name": "splice_ai_donor_gain_distance", + "type": "Integer", + "mode": "Nullable" + }, + { + "description": "Slice AI", + "name": "splice_ai_donor_loss_score", + "type": "Float", + "mode": "Nullable" + }, + { + "description": "Slice AI", + "name": "splice_ai_donor_loss_distance", + "type": "Integer", + "mode": "Nullable" + }, + { + "description": "ClinVar Classification", + "name": "clinvar_classification", + "type": "String", + "mode": "Nullable" + }, + { + "description": "ClinVar Classification Date", + "name": "clinvar_last_updated", + "type": "Date", + "mode": "Nullable" + }, + { + "description": "ClinVar Disease Name", + "name": "clinvar_phenotype", + "type": "String", + "mode": "Repeated" + }, + { + "description": "gnomAD: 'Total' frequency", + "name": "gnomad_all_af", + "type": "Float", + "mode": "Nullable" + }, + { + "description": "gnomAD: 'Total' allele count", + "name": "gnomad_all_ac", + "type": "Integer", + "mode": "Nullable" + }, + { + "description": "gnomAD: 'Total' allele number", + "name": "gnomad_all_an", + "type": "Integer", + "mode": "Nullable" + }, + { + "description": "gnomAD: Max subpopulation frequency", + "name": "gnomad_max_af", + "type": "Float", + "mode": "Nullable" + }, + { + "description": "gnomAD: Max subpopulation count", + "name": "gnomad_max_ac", + "type": "Integer", + "mode": "Nullable" + }, + { + "description": "gnomAD: Max subpopulation number", + "name": "gnomad_max_an", + "type": "Integer", + "mode": "Nullable" + }, + { + "description": "gnomAD: Max subpopulation ethnicity", + "name": "gnomad_max_subpop", + "type": "String", + "mode": "Nullable" + }, + { + "description": "OMIM ID", + "name": "gene_omim_id", + "type": "Integer", + "mode": "Nullable" + }, + { + "description": "OMIM Disease ID TODO -- this needs to be swapped to Repeated not nullable", + "name": "omim_phenotypes_id", + "type": "Integer", + "mode": "Nullable" + }, + { + "description": "OMIM Disease Name TODO -- this needs to be swapped to Repeated not nullable", + "name": "omim_phenotypes_name", + "type": "String", + "mode": "Nullable" + } + ]' + File? gatk_override } @@ -18,6 +286,7 @@ workflow GvsSitesOnlyVCF { } call MergeVCFs { # why are we merging before annotating? couldn't we keep them separate? + # I guess if we create the table in one single thread, we can load data w multi (we would be downloading the annotations many times perhaps...) input: input_vcfs = SitesOnlyVcf.output_vcf, input_vcf_indices = SitesOnlyVcf.output_vcf_idx, @@ -30,8 +299,18 @@ workflow GvsSitesOnlyVCF { output_annotated_file_name = output_annotated_file_name, nirvana_data_tar = nirvana_data_directory } + + call BigQueryLoadJson { + input: + annotation_json = AnnotateVCF.annotation_json, + annotation_json_jsi = AnnotateVCF.annotation_json_jsi, + nirvana_schema = nirvana_schema, + project_id = project_id + } } + + ################################################################################ task SitesOnlyVcf { input { @@ -144,4 +423,112 @@ task AnnotateVCF { } } +task BigQueryLoadJson { + input { + File annotation_json + File annotation_json_jsi + String nirvana_schema + String project_id + } + command <<< + set -e + + # prepare the json file for loading into BQ by making it a new line delimited json + jq -c '.positions | .[]' ~{annotation_json} > load_into_bq.json + + # load this json in as a temp interim BQ vat table + $TEMP_TABLE="~{dataset_name}.pre-vat" + bq --location=US load --project_id=~{project_id} --source_format=NEWLINE_DELIMITED_JSON --autodetect $TEMP_TABLE load_into_bq.json + + + # make the BQ vat table (this will help with validation) + PARTITION_FIELD="position" + CLUSTERING_FIELD="vid" + PARTITION_STRING="--range_partitioning=$PARTITION_FIELD,0,4000,4000" + CLUSTERING_STRING="--clustering_fields=$CLUSTERING_FIELD" + TABLE="~{dataset_name}.vatter" + SCHEMA="~{nirvana_schema}" + PROJECT="~{project_id}" + + # bq --location=US mk --project_id="spec-ops-aou" "anvil_100_for_testing.vat" "scripts/variantstore/wdl/schemas/vat_schema.json" + bq --location=US mk ${PARTITION_STRING} ${CLUSTERING_STRING} --project_id=~{project_id} $TABLE $SCHEMA > status_bq_submission + + # now run some giant query in BQ to get this all in the right table + bq query --destination_table=$TABLE \ + 'SELECT + v.position, + v.vid, + v.chromosome AS contig, + v.refAllele AS ref_allele, + v.altAllele AS alt_allele, + v.variantType AS variant_type, + v.hgvsg AS genomic_location, + v.dbsnp AS dbsnp_rsid, + t.transcript, + t.hgnc AS gene_symbol, + t.source AS transcript_source, + t.hgvsp AS aa_change, + t.consequence as consequence, # gross, + t.hgvsc AS dna_change, + t.exons AS exon_number, + t.introns AS intron_number, + t.hgvsc AS splice_distance, + t.geneId AS entrez_gene_id, + CASE WHEN ( v.transcript is not null and t.isCanonical is not True) THEN False WHEN ( v.transcript is not null and t.isCanonical is True) THEN True END AS is_canonical_transcript, + null AS gvs_all_ac, # what is this mapping? + null AS gvs_all_an, + null AS gvs_all_af, + v.revel.score AS revel, + # we just grab the first value in spliceAI (need to validate that there will only ever be one) + CASE WHEN (select array_length(v.spliceAI)) > 0 + THEN v.spliceAI[offset(0)].acceptorGainScore END AS splice_ai_acceptor_gain_score, + CASE WHEN (select array_length(v.spliceAI)) > 0 + THEN v.spliceAI[offset(0)].acceptorGainDistance END AS splice_ai_acceptor_gain_distance, + CASE WHEN (select array_length(v.spliceAI)) > 0 + THEN v.spliceAI[offset(0)].acceptorLossScore END AS splice_ai_acceptor_loss_score, + CASE WHEN (select array_length(v.spliceAI)) > 0 + THEN v.spliceAI[offset(0)].acceptorLossDistance END AS splice_ai_acceptor_loss_distance, + CASE WHEN (select array_length(v.spliceAI)) > 0 + THEN v.spliceAI[offset(0)].donorGainScore END AS splice_ai_donor_gain_score, + CASE WHEN (select array_length(v.spliceAI)) > 0 + THEN v.spliceAI[offset(0)].donorGainDistance END AS splice_ai_donor_gain_distance, + CASE WHEN (select array_length(v.spliceAI)) > 0 + THEN v.spliceAI[offset(0)].donorLossScore END AS splice_ai_donor_loss_score, + CASE WHEN (select array_length(v.spliceAI)) > 0 + THEN v.spliceAI[offset(0)].donorLossDistance END AS splice_ai_donor_loss_distance, + (SELECT significance[offset(0)] FROM v.clinvar WHERE id LIKE "RCV%") AS clinvar_classification, + (SELECT lastUpdatedDate FROM v.clinvar WHERE id LIKE "RCV%") AS clinvar_last_updated, + (SELECT phenotypes FROM v.clinvar WHERE id LIKE "RCV%") AS clinvar_phenotype, + v.gnomad.allAf AS gnomad_all_af, + v.gnomad.allAc AS gnomad_all_ac, + v.gnomad.allAn AS gnomad_all_an, + v.gnomad.afrAf AS gnomad_max_af, + v.gnomad.afrAc AS gnomad_max_ac, + v.gnomad.afrAn AS gnomad_max_an, + null AS gnomad_max_subpop, # what is this mapping? + null AS gene_omim_id, + null AS omim_phenotypes_id, + null AS omim_phenotypes_name, + from (SELECT position, variantline.* FROM $PROJECT.$TABLE, UNNEST(variants) as variantline) as a left join + (SELECT position, variantline.vid, transcriptline.* FROM $PROJECT.$TABLE, UNNEST(variants) as variantline, UNNEST(variantline.transcripts) as transcriptline) as b on a.vid = b.vid)' + + cat status_bq_submission | tail -n 1 > status_bq_submission_last_line + bq_job_id=$(sed 's/.*://' status_bq_submission_last_line) + echo $bq_job_id + >>> + # ------------------------------------------------ + # Runtime settings: + runtime { + docker: "broadinstitute/gatk:4.2.0.0" + memory: "3 GB" + cpu: "1" + disks: "local-disk 100 HDD" + } + # ------------------------------------------------ + # Outputs: + output { + Boolean done = true + } +} + From eef77b5a95bea183d52409700434a0fc3f1cfe45 Mon Sep 17 00:00:00 2001 From: rori <6863459+RoriCremer@users.noreply.github.com> Date: Wed, 16 Jun 2021 01:33:23 -0400 Subject: [PATCH 11/73] prob not to keep--maybe for testing --- .../create_variant_annotation_table.py | 603 +++++++----------- 1 file changed, 242 insertions(+), 361 deletions(-) diff --git a/scripts/variantstore/wdl/extract/create_variant_annotation_table.py b/scripts/variantstore/wdl/extract/create_variant_annotation_table.py index 6b44c34a139..72d3f15fbb1 100644 --- a/scripts/variantstore/wdl/extract/create_variant_annotation_table.py +++ b/scripts/variantstore/wdl/extract/create_variant_annotation_table.py @@ -7,379 +7,260 @@ from google.cloud.bigquery.job import QueryJobConfig from google.oauth2 import service_account -import argparse -import re +import csv +import json + JOB_IDS = set() # # CONSTANTS # -PET_TABLE_PREFIX = "pet_" -VET_TABLE_PREFIX = "vet_" +VAT_TABLE_PREFIX = "vat_" SAMPLES_PER_PARTITION = 4000 -FINAL_TABLE_TTL = "" -#FINAL_TABLE_TTL = " OPTIONS( expiration_timestamp=TIMESTAMP_ADD(CURRENT_TIMESTAMP(), INTERVAL 72 HOUR)) " - -# temp-table-uuid -output_table_prefix = str(uuid.uuid4()).split("-")[0] -print(f"running with prefix {output_table_prefix}") - -PET_VET_TABLE_COUNT = -1 -client = None - -VET_DISTINCT_POS_TABLE = f"{output_table_prefix}_vet_distinct_pos" -PET_NEW_TABLE = f"{output_table_prefix}_pet_new" -VET_NEW_TABLE = f"{output_table_prefix}_vet_new" -EXTRACT_SAMPLE_TABLE = f"{output_table_prefix}_sample_names" - -def utf8len(s): - return len(s.encode('utf-8')) - -def dump_job_stats(): - total = 0 - - for jobid in JOB_IDS: - job = client.get_job(jobid[1]) - - bytes_billed = int(0 if job.total_bytes_billed is None else job.total_bytes_billed) - total = total + bytes_billed - - print(jobid[0], " <====> Cache Hit:", job.cache_hit, bytes_billed/(1024 * 1024), " MBs") - - print(" Total GBs billed ", total/(1024 * 1024 * 1024), " GBs") - -def execute_with_retry(label, sql): - retry_delay = [30, 60, 90] # 3 retries with incremental backoff - start = time.time() - while len(retry_delay) > 0: - try: - query_label = label.replace(" ","-").strip().lower() - - existing_labels = client._default_query_job_config.labels - job_labels = existing_labels - job_labels["gvs_query_name"] = query_label - job_config = bigquery.QueryJobConfig(labels=job_labels) - query = client.query(sql, job_config=job_config) - - print(f"STARTING - {label}") - JOB_IDS.add((label, query.job_id)) - results = query.result() - print(f"COMPLETED ({time.time() - start} s, {3-len(retry_delay)} retries) - {label}") - return results - except Exception as err: - # if there are no retries left... raise - if (len(retry_delay) == 0): - raise err - else: - t = retry_delay.pop(0) - print(f"Error {err} running query {label}, sleeping for {t}") - time.sleep(t) - -def get_partition_range(i): - if i < 1 or i > PET_VET_TABLE_COUNT: - raise ValueError(f"out of partition range") - - return { 'start': (i-1)*SAMPLES_PER_PARTITION + 1, 'end': i*SAMPLES_PER_PARTITION } - -def get_samples_for_partition(sample_ids, i): - return [ s for s in sample_ids if s >= get_partition_range(i)['start'] and s <= get_partition_range(i)['end'] ] - -def split_lists(samples, n): - return [samples[i * n:(i + 1) * n] for i in range((len(samples) + n - 1) // n )] - -def load_sample_names(sample_names_to_extract, fq_temp_table_dataset): - schema = [ bigquery.SchemaField("sample_name", "STRING", mode="REQUIRED") ] - fq_sample_table = f"{fq_temp_table_dataset}.{EXTRACT_SAMPLE_TABLE}" - - job_labels = client._default_query_job_config.labels - job_labels["gvs_query_name"] = "load-sample-names" - - job_config = bigquery.LoadJobConfig(source_format=bigquery.SourceFormat.CSV, skip_leading_rows=0, schema=schema, labels=job_labels) - - with open(sample_names_to_extract, "rb") as source_file: - job = client.load_table_from_file(source_file, fq_sample_table, job_config=job_config) - - job.result() # Waits for the job to complete. - - # setting the TTL needs to be done as a second API call - table = bigquery.Table(fq_sample_table, schema=schema) - expiration = datetime.datetime.utcnow() + datetime.timedelta(hours=TEMP_TABLE_TTL_HOURS) - table.expires = expiration - table = client.update_table(table, ["expires"]) - - return fq_sample_table - -def get_all_sample_ids(fq_destination_table_samples): - sql = f"select sample_id from `{fq_destination_table_samples}`" - - results = execute_with_retry("read cohort sample table", sql) - sample_ids = [row.sample_id for row in list(results)] - sample_ids.sort() - return sample_ids - -def create_extract_samples_table(fq_destination_table_samples, fq_sample_name_table, fq_sample_mapping_table): - sql = f"CREATE OR REPLACE TABLE `{fq_destination_table_samples}` AS (" \ - f"SELECT m.sample_id, m.sample_name FROM `{fq_sample_name_table}` s JOIN `{fq_sample_mapping_table}` m ON (s.sample_name = m.sample_name) )" - - results = execute_with_retry("create extract sample table", sql) - return results - -def get_table_count(fq_pet_vet_dataset): - sql = f"SELECT MAX(CAST(SPLIT(table_name, '_')[OFFSET(1)] AS INT64)) max_table_number " \ - f"FROM `{fq_pet_vet_dataset}.INFORMATION_SCHEMA.TABLES` " \ - f"WHERE REGEXP_CONTAINS(lower(table_name), r'^(pet_[0-9]+)$') " - results = execute_with_retry("get max table", sql) - return int([row.max_table_number for row in list(results)][0]) - -def make_new_vet_union_all(fq_pet_vet_dataset, fq_temp_table_dataset, sample_ids): - def get_subselect(fq_vet_table, samples, id): - sample_stanza = ','.join([str(s) for s in samples]) - sql = f" q_{id} AS (SELECT location, sample_id, ref, alt, call_GT, call_GQ, call_pl, QUALapprox, AS_QUALapprox from `{fq_vet_table}` WHERE sample_id IN ({sample_stanza})), " - return sql - - subs = {} - for i in range(1, PET_VET_TABLE_COUNT+1): - partition_samples = get_samples_for_partition(sample_ids, i) - - # KCIBUL -- grr, should be fixed width - fq_vet_table = f"{fq_pet_vet_dataset}.{VET_TABLE_PREFIX}{i:03}" - if len(partition_samples) > 0: - j = 1 - for samples in split_lists(partition_samples, 1000): - id = f"{i}_{j}" - subs[id] = get_subselect(fq_vet_table, samples, id) - j = j + 1 - - sql = f"create or replace table `{fq_temp_table_dataset}.{VET_NEW_TABLE}` {TEMP_TABLE_TTL} AS \n" + \ - "with\n" + \ - ("\n".join(subs.values())) + "\n" \ - "q_all AS (" + (" union all ".join([ f"(SELECT * FROM q_{id})" for id in subs.keys()])) + ")\n" + \ - f" (SELECT * FROM q_all)" - - print(sql) - print(f"VET Query is {utf8len(sql)/(1024*1024)} MB in length") - results = execute_with_retry("insert vet new table", sql) - return results - - - -def create_position_table(fq_temp_table_dataset, min_variant_samples): - dest = f"{fq_temp_table_dataset}.{VET_DISTINCT_POS_TABLE}" - - # only create this clause if min_variant_samples > 0, because if - # it is == 0 then we don't need to touch the sample_id column (which doubles the cost of this query) - min_sample_clause = "" - if min_variant_samples > 0: - min_sample_clause = f"HAVING count(distinct sample_id) >= {min_variant_samples}" - - sql = f""" - create or replace table `{dest}` {TEMP_TABLE_TTL} - as ( - select location from `{fq_temp_table_dataset}.{VET_NEW_TABLE}` WHERE alt != '*' GROUP BY location {min_sample_clause} - ) - """ - existing_labels = client._default_query_job_config.labels - job_labels = existing_labels - job_labels["gvs_query_name"] = "create-position-table" - job_config = bigquery.QueryJobConfig(labels=job_labels) - create_vet_distinct_pos_query = client.query(sql, job_config=job_config) - - create_vet_distinct_pos_query.result() - JOB_IDS.add((f"create positions table {dest}", create_vet_distinct_pos_query.job_id)) - return - -def make_new_pet_union_all(fq_pet_vet_dataset, fq_temp_table_dataset, sample_ids): - def get_pet_subselect(fq_pet_table, samples, id): - sample_stanza = ','.join([str(s) for s in samples]) - sql = f" q_{id} AS (SELECT p.location, p.sample_id, p.state from {fq_pet_table} p " \ - f" join `{fq_temp_table_dataset}.{VET_DISTINCT_POS_TABLE}` v on (p.location = v.location) WHERE p.sample_id IN ({sample_stanza})), " - return sql - - subs = {} - for i in range(1, PET_VET_TABLE_COUNT+1): - partition_samples = get_samples_for_partition(sample_ids, i) - - # KCIBUL -- grr, should be fixed width - fq_pet_table = f"{fq_pet_vet_dataset}.{PET_TABLE_PREFIX}{i:03}" - if len(partition_samples) > 0: - j = 1 - for samples in split_lists(partition_samples, 1000): - id = f"{i}_{j}" - subs[id] = get_pet_subselect(fq_pet_table, samples, id) - j = j + 1 - - sql = f"create or replace table `{fq_temp_table_dataset}.{PET_NEW_TABLE}` {TEMP_TABLE_TTL} AS \n" + \ - "with\n" + \ - ("\n".join(subs.values())) + "\n" \ - "q_all AS (" + (" union all ".join([ f"(SELECT * FROM q_{id})" for id in subs.keys()])) + ")\n" + \ - f" (SELECT * FROM q_all)" - - print(sql) - print(f"PET Query is {utf8len(sql)/(1024*1024)} MB in length") - results = execute_with_retry("insert pet new table", sql) - return results - - -def populate_final_extract_table(fq_temp_table_dataset, fq_destination_table_data, fq_sample_mapping_table): - sql = f""" - CREATE OR REPLACE TABLE `{fq_destination_table_data}` - PARTITION BY RANGE_BUCKET(location, GENERATE_ARRAY(0, 26000000000000, 6500000000)) - CLUSTER BY location - {FINAL_TABLE_TTL} - as (SELECT - new_pet.location, - s.sample_name as sample_name, - new_pet.state, - new_vet.ref, - REPLACE(new_vet.alt,",","") alt, - new_vet.call_GT, - new_vet.call_GQ, - cast(SPLIT(new_vet.call_pl,",")[OFFSET(0)] as int64) as call_RGQ, - new_vet.QUALapprox, - new_vet.AS_QUALapprox, - new_vet.call_PL - FROM - `{fq_temp_table_dataset}.{PET_NEW_TABLE}` new_pet - LEFT OUTER JOIN - `{fq_temp_table_dataset}.{VET_NEW_TABLE}` new_vet - ON (new_pet.location = new_vet.location AND new_pet.sample_id = new_vet.sample_id) - LEFT OUTER JOIN - `{fq_sample_mapping_table}` s ON (new_pet.sample_id = s.sample_id)) - """ - print(sql) - existing_labels = client._default_query_job_config.labels - job_labels = existing_labels - job_labels["gvs_query_name"] = "populate-final-extract-table" - job_config = bigquery.QueryJobConfig(labels=job_labels) - cohort_extract_final_query_job = client.query(sql, job_config=job_config) - - cohort_extract_final_query_job.result() - JOB_IDS.add((f"insert final cohort table {fq_destination_table_data}", cohort_extract_final_query_job.job_id)) - return - -def make_extract_table(fq_pet_vet_dataset, - max_tables, - sample_names_to_extract, - fq_cohort_sample_names, - query_project, - query_labels, - fq_temp_table_dataset, - fq_destination_dataset, - destination_table_prefix, - min_variant_samples, - fq_sample_mapping_table, - sa_key_path, - temp_table_ttl_hours - ): - try: - fq_destination_table_data = f"{fq_destination_dataset}.{destination_table_prefix}__DATA" - fq_destination_table_samples = f"{fq_destination_dataset}.{destination_table_prefix}__SAMPLES" - - global client - # this is where a set of labels are being created for the cohort extract - query_labels_map = {} - query_labels_map["id"]= output_table_prefix - query_labels_map["gvs_tool_name"]= "gvs_prepare_callset" - - # query_labels is string that looks like 'key1=val1, key2=val2' - if query_labels is not None and len(query_labels) != 0: - for query_label in query_labels: - kv = query_label.split("=", 2) - key = kv[0].strip().lower() - value = kv[1].strip().lower() - query_labels_map[key] = value - - if not (bool(re.match(r"[a-z0-9_-]+$", key)) & bool(re.match(r"[a-z0-9_-]+$", value))): - raise ValueError(f"label key or value did not pass validation--format should be 'key1=val1, key2=val2'") - - #Default QueryJobConfig will be merged into job configs passed in - #but if a specific default config is being updated (eg labels), new config must be added - #to the client._default_query_job_config that already exists - default_config = QueryJobConfig(labels=query_labels_map, priority="INTERACTIVE", use_query_cache=False) - - if sa_key_path: - credentials = service_account.Credentials.from_service_account_file( - sa_key_path, scopes=["https://www.googleapis.com/auth/cloud-platform"], - ) - - client = bigquery.Client(credentials=credentials, - project=query_project, - default_query_job_config=default_config) - else: - client = bigquery.Client(project=query_project, - default_query_job_config=default_config) - - ## TODO -- provide a cmdline arg to override this (so we can simulate smaller datasets) - - global PET_VET_TABLE_COUNT - PET_VET_TABLE_COUNT = max_tables - - global TEMP_TABLE_TTL_HOURS - TEMP_TABLE_TTL_HOURS = temp_table_ttl_hours - - global TEMP_TABLE_TTL - TEMP_TABLE_TTL = f" OPTIONS( expiration_timestamp=TIMESTAMP_ADD(CURRENT_TIMESTAMP(), INTERVAL {TEMP_TABLE_TTL_HOURS} HOUR)) " - - print(f"Using {PET_VET_TABLE_COUNT} PET tables in {fq_pet_vet_dataset}...") - - # if we have a file of sample names, load it into a temporary table - if (sample_names_to_extract): - fq_sample_name_table = load_sample_names(sample_names_to_extract, fq_temp_table_dataset) - else: - fq_sample_name_table = fq_cohort_sample_names - - # At this point one way or the other we have a table of sample names in BQ, - # join it to the sample_info table to drive the extract - create_extract_samples_table(fq_destination_table_samples, fq_sample_name_table, fq_sample_mapping_table) - - # pull the sample ids back down - sample_ids = get_all_sample_ids(fq_destination_table_samples) - print(f"Discovered {len(sample_ids)} samples in {fq_destination_table_samples}...") - - make_new_vet_union_all(fq_pet_vet_dataset, fq_temp_table_dataset, sample_ids) - - create_position_table(fq_temp_table_dataset, min_variant_samples) - make_new_pet_union_all(fq_pet_vet_dataset, fq_temp_table_dataset, sample_ids) - populate_final_extract_table(fq_temp_table_dataset, fq_destination_table_data, fq_destination_table_samples) - finally: - dump_job_stats() - - print(f"\nFinal cohort extract data written to {fq_destination_table_data}\n") - -if __name__ == '__main__': +vat_nirvana_positions_dictionary = { + "position": "position", # required TODO pull this out! check how nirvana handles "when the vcf position is not just the preceeding base for the variant" +} + +vat_nirvana_variants_dictionary = { + "vid": "vid", # required + "contig": "chromosome", # required + "ref_allele": "refAllele", # required + "alt_allele": "altAllele", # required + "variant_type": "variantType", # required + "genomic_location": "hgvsg", # required + "dbsnp_rsid": "dbsnp", # nullable -- TODO is this always a single val array? +} + +vat_nirvana_transcripts_dictionary = { + "transcript": "transcript", # nullable + "gene_symbol": "hgnc", # nullable + "transcript_source": "source", # nullable + "aa_change": "hgvsp", # nullable + "consequence": "consequence", # nullable -- TODO check on this one. May want this to be "[]" + "dna_change": "hgvsc", # nullable + "exon_number": "exons", # nullable + "intron_number": "introns", # nullable + "splice_distance": "hgvsc", # nullable -- TODO Additional processing: Extract the splice distance from the hgvsc field + "entrez_gene_id": "geneId", # nullable + # "hgnc_gene_id": "hgncid", # nullable -- TODO ignore for now Lees notes dont match up here: genes.hgncid? + "is_canonical_transcript": "isCanonical" # nullable -- (and lets make the nulls false) +} + +vat_nirvana_gvs_alleles_dictionary = { + "gvs_all_ac": "x", # required + "gvs_all_an": "x", # required + "gvs_all_af": "x" # required +} + +vat_nirvana_revel_dictionary = { + "revel": "score" # nullable +} + +vat_nirvana_splice_ai_dictionary = { + "splice_ai_acceptor_gain_score": "acceptorGainScore", # nullable + "splice_ai_acceptor_gain_distance": "acceptorGainDistance", # nullable + "splice_ai_acceptor_loss_score": "acceptorLossScore", # nullable + "splice_ai_acceptor_loss_distance": "acceptorLossDistance", # nullable + "splice_ai_donor_gain_score": "donorGainScore", # nullable + "splice_ai_donor_gain_distance": "donorGainDistance", # nullable + "splice_ai_donor_loss_score": "donorLossScore", # nullable + "splice_ai_donor_loss_distance": "donorLossDistance" # nullable +} + +vat_nirvana_clinvar_dictionary = { + "clinvar_classification": "significance", # nullable + "clinvar_last_updated": "lastUpdatedDate", # nullable + "clinvar_phenotype": "phenotypes" # nullable -- currently here: "phenotypes":["not specified"] <-- lets talk arrays! +} + +vat_nirvana_gnomad_dictionary = { + "gnomad_all_af": "allAf", # nullable + "gnomad_all_ac": "allAc", # nullable + "gnomad_all_an": "allAn", # nullable + "gnomad_max_af": "afrAf", # nullable + "gnomad_max_ac": "afrAc", # nullable + "gnomad_max_an": "afrAn", # nullable + "gnomad_max_subpop": "x" #TODO need to choose the correct mapping. Lee says maybe drop for now +} + +vat_nirvana_omim_dictionary = { # TODO or should this be vat_nirvana_genes_dictionary ? + "gene_omim_id": "mimNumber", # nullable + "omim_phenotypes_id": "phenotype", # nullable <-- lets talk arrays! + "omim_phenotypes_name": "x" #TODO where is the omim stuff?????? <-- lets talk arrays! +} + +def make_fieldnames(): + positions_fieldnames = list(vat_nirvana_positions_dictionary.keys()) + variants_fieldnames = list(vat_nirvana_variants_dictionary.keys()) + transcripts_fieldnames = list(vat_nirvana_transcripts_dictionary.keys()) + gvs_alleles_fieldnames = list(vat_nirvana_gvs_alleles_dictionary.keys()) + revel_fieldnames = list(vat_nirvana_revel_dictionary) + splice_ai_fieldnames = list(vat_nirvana_splice_ai_dictionary.keys()) + clinvar_fieldnames = list(vat_nirvana_clinvar_dictionary.keys()) + gnomad_fieldnames = list(vat_nirvana_gnomad_dictionary.keys()) + omim_fieldnames = list(vat_nirvana_omim_dictionary.keys()) + + return positions_fieldnames, variants_fieldnames, transcripts_fieldnames, gvs_alleles_fieldnames, revel_fieldnames, splice_ai_fieldnames, clinvar_fieldnames, gnomad_fieldnames, omim_fieldnames + + + +def make_annotated_row(row_position, variant_line, transcript_line): # would it be better to not pass the transcript_line since its dupe data? + positions_fieldnames, variants_fieldnames, transcripts_fieldnames, gvs_alleles_fieldnames, revel_fieldnames, splice_ai_fieldnames, clinvar_fieldnames, gnomad_fieldnames, omim_fieldnames = make_fieldnames() + row = {} + row["position"] = row_position # this is a required field -- do we want validation? (what about validation for all the variants_fieldnames?) + + for vat_variants_fieldname in variants_fieldnames: # like "contig" + nirvana_variants_fieldname = vat_nirvana_variants_dictionary.get(vat_variants_fieldname) + variant_fieldvalue = variant_line.get(nirvana_variants_fieldname) + row[vat_variants_fieldname] = variant_fieldvalue + + if transcript_line != None: + for vat_transcripts_fieldname in transcripts_fieldnames: # like "transcript" + nirvana_transcripts_fieldname = vat_nirvana_transcripts_dictionary.get(vat_transcripts_fieldname) + transcript_fieldvalue = transcript_line.get(nirvana_transcripts_fieldname) + if nirvana_transcripts_fieldname = "isCanonical" & transcript_fieldvalue != True: # oooof this is ugly + transcript_fieldvalue = False + row[vat_transcripts_fieldname] = transcript_fieldvalue + + for vat_gvs_alleles_fieldname in gvs_alleles_fieldnames: # like "gvs_all_ac" + nirvana_gvs_alleles_fieldname = vat_nirvana_gvs_alleles_dictionary.get(vat_gvs_alleles_fieldname) + gvs_alleles_fieldvalue = variant_line.get(nirvana_gvs_alleles_fieldname) + row[vat_gvs_alleles_fieldname] = gvs_alleles_fieldvalue + + if variant_line.get("gnomad") != None: + for vat_gnomad_fieldname in gnomad_fieldnames: # like "gnomad_all_af" + nirvana_gnomad_fieldname = vat_nirvana_gnomad_dictionary.get(vat_gnomad_fieldname) + gnomad_fieldvalue = variant_line.get("gnomad").get(nirvana_gnomad_fieldname) # not a list like the others + row[vat_gnomad_fieldname] = gnomad_fieldvalue + + if variant_line.get("spliceAI") != None: + splice_ai_line = variant_line["spliceAI"][0] # TODO I am making the huge assumption that we are only grabbing 1 + for vat_splice_ai_fieldname in splice_ai_fieldnames: # like "splice_ai_acceptor_gain_score" + nirvana_splice_ai_fieldname = vat_nirvana_splice_ai_dictionary.get(vat_splice_ai_fieldname) + splice_ai_fieldvalue = splice_ai_line.get(nirvana_splice_ai_fieldname) + row[vat_splice_ai_fieldname] = splice_ai_fieldvalue + + if variant_line.get("clinvar") != None: + clinvar_line = variant_line["clinvar"][0] # TODO I am making the huge assumption that we are only grabbing 1 + for vat_clinvar_fieldname in clinvar_fieldnames: # like "clinvar_classification" + nirvana_clinvar_fieldname = vat_nirvana_clinvar_dictionary.get(vat_clinvar_fieldname) + clinvar_fieldvalue = clinvar_line.get(nirvana_clinvar_fieldname) + row[vat_clinvar_fieldname] = clinvar_fieldvalue + + if variant_line.get("genes") != None: + omim_line = variant_line["genes"][0] # TODO I am making the huge assumption that we are only grabbing 1 + for vat_omim_fieldname in omim_fieldnames: # like "clinvar_classification" + nirvana_omim_fieldname = vat_nirvana_omim_dictionary.get(vat_omim_fieldname) + omim_fieldvalue = omim_line.get(nirvana_omim_fieldname) + row[vat_omim_fieldname] = omim_fieldvalue + + if variant_line.get("revel") != None: + row["revel"] = variant_line.get("revel").get("score") + + return row + +def make_annotation_table(annotated_json, output_csv): + with open(output_csv, 'w', newline='') as csvfile: + positions_fieldnames, variants_fieldnames, transcripts_fieldnames, gvs_alleles_fieldnames, revel_fieldnames, splice_ai_fieldnames, clinvar_fieldnames, gnomad_fieldnames, omim_fieldnames = make_fieldnames() + fieldnames = positions_fieldnames + fieldnames.extend(variants_fieldnames) + fieldnames.extend(transcripts_fieldnames) + fieldnames.extend(gvs_alleles_fieldnames) + fieldnames.extend(revel_fieldnames) + fieldnames.extend(splice_ai_fieldnames) + fieldnames.extend(clinvar_fieldnames) + fieldnames.extend(gnomad_fieldnames) + fieldnames.extend(omim_fieldnames) + writer = csv.DictWriter(csvfile, fieldnames=fieldnames) + + writer.writeheader() + # in the future can we simplify this pre-processing? + json_data = open(annotated_json) + data = json.load(json_data) + annotated_json_lines = data["positions"] + for annotated_json_line in annotated_json_lines: + row_position = annotated_json_line.get("position") # this is a required field -- do we want validation? + # want to write a csv row for each variant - transcript + # so let's start with each variant + variant_lines = annotated_json_line.get("variants") # this is a required field -- do we want validation? + for variant_line in variant_lines: + if variant_line.get("transcripts") == None: + # then we make a special row + print("can I handle this?") + row = make_annotated_row(row_position, variant_line, None) + print("could I handle this?") + print(row) + writer.writerow(row) + else: + transcript_lines = variant_line.get("transcripts") + for transcript_line in transcript_lines: + row = make_annotated_row(row_position, variant_line, transcript_line) + print(row) + writer.writerow(row) + +""" row = {} + row["position"] = annotated_json_line.get("position") # this is a required field -- do we want validation? (what about validation for all the variants_fieldnames?) + + for vat_variants_fieldname in variants_fieldnames: # like "contig" + nirvana_variants_fieldname = vat_nirvana_variants_dictionary.get(vat_variants_fieldname) + variant_fieldvalue = variant_line.get(nirvana_variants_fieldname) + row[vat_variants_fieldname] = variant_fieldvalue + + for vat_transcripts_fieldname in transcripts_fieldnames: # like "transcript" + nirvana_transcripts_fieldname = vat_nirvana_transcripts_dictionary.get(vat_transcripts_fieldname) + transcript_fieldvalue = transcript_line.get(nirvana_transcripts_fieldname) + row[vat_transcripts_fieldname] = transcript_fieldvalue + + for vat_gvs_alleles_fieldname in gvs_alleles_fieldnames: # like "gvs_all_ac" + nirvana_gvs_alleles_fieldname = vat_nirvana_gvs_alleles_dictionary.get(vat_gvs_alleles_fieldname) + gvs_alleles_fieldvalue = variant_line.get(nirvana_gvs_alleles_fieldname) + row[vat_gvs_alleles_fieldname] = gvs_alleles_fieldvalue + + if variant_line.get("gnomad") != None: + for vat_gnomad_fieldname in gnomad_fieldnames: # like "gnomad_all_af" + nirvana_gnomad_fieldname = vat_nirvana_gnomad_dictionary.get(vat_gnomad_fieldname) + gnomad_fieldvalue = variant_line.get("gnomad").get(nirvana_gnomad_fieldname) # not a list like the others + row[vat_gnomad_fieldname] = gnomad_fieldvalue + + if variant_line.get("spliceAI") != None: + splice_ai_line = variant_line["spliceAI"][0] # TODO I am making the huge assumption that we are only grabbing 1 + for vat_splice_ai_fieldname in splice_ai_fieldnames: # like "splice_ai_acceptor_gain_score" + nirvana_splice_ai_fieldname = vat_nirvana_splice_ai_dictionary.get(vat_splice_ai_fieldname) + splice_ai_fieldvalue = splice_ai_line.get(nirvana_splice_ai_fieldname) + row[vat_splice_ai_fieldname] = splice_ai_fieldvalue + + if variant_line.get("clinvar") != None: + clinvar_line = variant_line["clinvar"][0] # TODO I am making the huge assumption that we are only grabbing 1 + for vat_clinvar_fieldname in clinvar_fieldnames: # like "clinvar_classification" + nirvana_clinvar_fieldname = vat_nirvana_clinvar_dictionary.get(vat_clinvar_fieldname) + clinvar_fieldvalue = clinvar_line.get(nirvana_clinvar_fieldname) + row[vat_clinvar_fieldname] = clinvar_fieldvalue + + if variant_line.get("genes") != None: + omim_line = variant_line["genes"][0] # TODO I am making the huge assumption that we are only grabbing 1 + for vat_omim_fieldname in omim_fieldnames: # like "clinvar_classification" + nirvana_omim_fieldname = vat_nirvana_omim_dictionary.get(vat_omim_fieldname) + omim_fieldvalue = omim_line.get(nirvana_omim_fieldname) + row[vat_omim_fieldname] = omim_fieldvalue + + if variant_line.get("revel") != None: + row["revel"] = variant_line.get("revel").get("score") + + + print(row) + writer.writerow(row)""" + + +""" if __name__ == '__main__': parser = argparse.ArgumentParser(allow_abbrev=False, description='Extract a cohort from BigQuery Variant Store ') - parser.add_argument('--fq_petvet_dataset',type=str, help='project.dataset location of pet/vet data', required=True) - parser.add_argument('--fq_temp_table_dataset',type=str, help='project.dataset location where results should be stored', required=True) - parser.add_argument('--fq_destination_dataset',type=str, help='project.dataset location where results should be stored', required=True) - parser.add_argument('--destination_cohort_table_prefix',type=str, help='prefix used for destination cohort extract tables (e.g. my_fantastic_cohort)', required=True) - parser.add_argument('--query_project',type=str, help='Google project where query should be executed', required=True) - parser.add_argument('--query_labels',type=str, action='append', help='Labels to put on the BQ query that will show up in the billing. Ex: --query_labels key1=value1 --query_labels key2=value2', required=False) - parser.add_argument('--min_variant_samples',type=int, help='Minimum variant samples at a site required to be emitted', required=False, default=0) - parser.add_argument('--fq_sample_mapping_table',type=str, help='Mapping table from sample_id to sample_name', required=True) - parser.add_argument('--sa_key_path',type=str, help='Path to json key file for SA', required=False) - parser.add_argument('--max_tables',type=int, help='Maximum number of PET/VET tables to consider', required=False, default=250) - parser.add_argument('--ttl',type=int, help='Temp table TTL in hours', required=False, default=72) - sample_args = parser.add_mutually_exclusive_group(required=True) - sample_args.add_argument('--sample_names_to_extract',type=str, help='File containing list of samples to extract, 1 per line') - sample_args.add_argument('--fq_cohort_sample_names',type=str, help='FQN of cohort table to extract, contains "sample_name" column') # Execute the parse_args() method args = parser.parse_args() - make_extract_table(args.fq_petvet_dataset, - args.max_tables, - args.sample_names_to_extract, - args.fq_cohort_sample_names, - args.query_project, - args.query_labels, - args.fq_temp_table_dataset, - args.fq_destination_dataset, - args.destination_cohort_table_prefix, - args.min_variant_samples, - args.fq_sample_mapping_table, - args.sa_key_path, - args.ttl) + make_annotation_table(annotated_json) """ + +make_annotation_table("hello_did_I_annotate.json", "vat_annotations.csv") From b6df3f9cf13b28818260bc299d8372ae6e645f87 Mon Sep 17 00:00:00 2001 From: rori <6863459+RoriCremer@users.noreply.github.com> Date: Wed, 16 Jun 2021 01:33:58 -0400 Subject: [PATCH 12/73] fixup on schema --- scripts/variantstore/wdl/schemas/vat_schema.json | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/scripts/variantstore/wdl/schemas/vat_schema.json b/scripts/variantstore/wdl/schemas/vat_schema.json index 38eea23fa57..aa3fe6b7cde 100644 --- a/scripts/variantstore/wdl/schemas/vat_schema.json +++ b/scripts/variantstore/wdl/schemas/vat_schema.json @@ -198,10 +198,10 @@ "mode": "Nullable" }, { - "description": "ClinVar Disease Name TODO -- this needs to be swapped to Repeated not nullable", + "description": "ClinVar Disease Name", "name": "clinvar_phenotype", "type": "String", - "mode": "Nullable" + "mode": "Repeated" }, { "description": "gnomAD: 'Total' frequency", From 58676c81354609a1f7f506c02318270dac21bd94 Mon Sep 17 00:00:00 2001 From: rori <6863459+RoriCremer@users.noreply.github.com> Date: Wed, 16 Jun 2021 02:12:44 -0400 Subject: [PATCH 13/73] add dataset --- scripts/variantstore/wdl/GvsSitesOnlyVCF.wdl | 274 +------------------ 1 file changed, 6 insertions(+), 268 deletions(-) diff --git a/scripts/variantstore/wdl/GvsSitesOnlyVCF.wdl b/scripts/variantstore/wdl/GvsSitesOnlyVCF.wdl index 5fcdc7d8866..45dbd5b15b6 100644 --- a/scripts/variantstore/wdl/GvsSitesOnlyVCF.wdl +++ b/scripts/variantstore/wdl/GvsSitesOnlyVCF.wdl @@ -6,274 +6,9 @@ workflow GvsSitesOnlyVCF { String output_merged_file_name String output_annotated_file_name String project_id + String dataset_name File nirvana_data_directory - String nirvana_schema = '[ - { - "description": "Must be positive. Exact position for a SNP and the position before the alteration in an indel", - "name": "position", - "type": "Integer", - "mode": "Required" - }, - { - "description": "Variant ID. Unique string for identifying a variant (as produced by NIRVANA based on a spec from Broad Institute)", - "name": "vid", - "type": "String", - "mode": "Required" - }, - { - "description": "Contig names match the hg38 reference", - "name": "contig", - "type": "String", - "mode": "Required" - }, - { - "description": "base(s). This should always be one base for SNPs and insertions. More than one base for deletions", - "name": "ref_allele", - "type": "String", - "mode": "Required" - }, - { - "description": "base(s). This should always be one base for SNPs and deletions. More than one base for insertions", - "name": "alt_allele", - "type": "String", - "mode": "Required" - }, - { - "description": "DNA change type (HGVS)", - "name": "variant_type", - "type": "String", - "mode": "Required" - }, - { - "description": "HGVS g. nomenclature Variant location", - "name": "genomic_location", - "type": "String", - "mode": "Required" - }, - { - "description": "rsID", - "name": "dbsnp_rsid", - "type": "String", - "mode": "Nullable" - }, - { - "description": "Transcript ID. Null indicates that this variant does not overlap any transcripts", - "name": "transcript", - "type": "String", - "mode": "Nullable" - }, - { - "description": "Gene symbol. A variant can have more than one associated gene symbol, since about 3% of genes do overlap", - "name": "gene_symbol", - "type": "String", - "mode": "Nullable" - }, - { - "description": "", - "name": "transcript_source", - "type": "String", - "mode": "Nullable" - }, - { - "description": "HGVS p. nomenclature; Amino acid change", - "name": "aa_change", - "type": "String", - "mode": "Nullable" - }, - { - "description": "Amino acid change type", - "name": "consequence", - "type": "String", - "mode": "Nullable" - }, - { - "description": "HGVS c. nomenclature; DNA change", - "name": "dna_change", - "type": "String", - "mode": "Nullable" - }, - { - "description": "Exon number", - "name": "exon_number", - "type": "String", - "mode": "Nullable" - }, - { - "description": "Intron number", - "name": "intron_number", - "type": "String", - "mode": "Nullable" - }, - { - "description": "Splice site distance for introns Will be a positive or negative integer", - "name": "splice_distance", - "type": "String", - "mode": "Nullable" - }, - { - "description": "Entrez/NCBI ID", - "name": "entrez_gene_id", - "type": "String", - "mode": "Nullable" - }, - { - "description": "Primary Transcript ID", - "name": "is_canonical_transcript", - "type": "String", - "mode": "Nullable" - }, - { - "description": "AC TODO -- this needs to be added back and swapped to required", - "name": "gvs_all_ac", - "type": "String", - "mode": "Nullable" - }, - { - "description": "AN TODO -- this needs to be added back and swapped to required", - "name": "gvs_all_an", - "type": "Integer", - "mode": "Nullable" - }, - { - "description": "AF TODO -- this needs to be added back and swapped to required", - "name": "gvs_all_af", - "type": "Float", - "mode": "Nullable" - }, - { - "description": "REVEL", - "name": "revel", - "type": "String", - "mode": "Nullable" - }, - { - "description": "Slice AI", - "name": "splice_ai_acceptor_gain_score", - "type": "Float", - "mode": "Nullable" - }, - { - "description": "Slice AI", - "name": "splice_ai_acceptor_gain_distance", - "type": "Integer", - "mode": "Nullable" - }, - { - "description": "Slice AI", - "name": "splice_ai_acceptor_loss_score", - "type": "Float", - "mode": "Nullable" - }, - { - "description": "Slice AI", - "name": "splice_ai_acceptor_loss_distance", - "type": "Integer", - "mode": "Nullable" - }, - { - "description": "Slice AI", - "name": "splice_ai_donor_gain_score", - "type": "Float", - "mode": "Nullable" - }, - { - "description": "Slice AI", - "name": "splice_ai_donor_gain_distance", - "type": "Integer", - "mode": "Nullable" - }, - { - "description": "Slice AI", - "name": "splice_ai_donor_loss_score", - "type": "Float", - "mode": "Nullable" - }, - { - "description": "Slice AI", - "name": "splice_ai_donor_loss_distance", - "type": "Integer", - "mode": "Nullable" - }, - { - "description": "ClinVar Classification", - "name": "clinvar_classification", - "type": "String", - "mode": "Nullable" - }, - { - "description": "ClinVar Classification Date", - "name": "clinvar_last_updated", - "type": "Date", - "mode": "Nullable" - }, - { - "description": "ClinVar Disease Name", - "name": "clinvar_phenotype", - "type": "String", - "mode": "Repeated" - }, - { - "description": "gnomAD: 'Total' frequency", - "name": "gnomad_all_af", - "type": "Float", - "mode": "Nullable" - }, - { - "description": "gnomAD: 'Total' allele count", - "name": "gnomad_all_ac", - "type": "Integer", - "mode": "Nullable" - }, - { - "description": "gnomAD: 'Total' allele number", - "name": "gnomad_all_an", - "type": "Integer", - "mode": "Nullable" - }, - { - "description": "gnomAD: Max subpopulation frequency", - "name": "gnomad_max_af", - "type": "Float", - "mode": "Nullable" - }, - { - "description": "gnomAD: Max subpopulation count", - "name": "gnomad_max_ac", - "type": "Integer", - "mode": "Nullable" - }, - { - "description": "gnomAD: Max subpopulation number", - "name": "gnomad_max_an", - "type": "Integer", - "mode": "Nullable" - }, - { - "description": "gnomAD: Max subpopulation ethnicity", - "name": "gnomad_max_subpop", - "type": "String", - "mode": "Nullable" - }, - { - "description": "OMIM ID", - "name": "gene_omim_id", - "type": "Integer", - "mode": "Nullable" - }, - { - "description": "OMIM Disease ID TODO -- this needs to be swapped to Repeated not nullable", - "name": "omim_phenotypes_id", - "type": "Integer", - "mode": "Nullable" - }, - { - "description": "OMIM Disease Name TODO -- this needs to be swapped to Repeated not nullable", - "name": "omim_phenotypes_name", - "type": "String", - "mode": "Nullable" - } - ]' - + String nirvana_schema = "position:INTEGER,vid:String,contig:STRING,ref_allele:STRING,alt_allele:STRING,variant_type:STRING,genomic_location:STRING,dbsnp_rsid:STRING,transcript:STRING,gene_symbol:STRING,transcript_source:STRING,aa_change:STRING,consequence:STRING,dna_change:String,exon_number:STRING,intron_number:STRING,splice_distance:STRING,entrez_gene_id:STRING,is_canonical_transcript:STRING,gvs_all_ac:STRING,gvs_all_an:STRING,gvs_all_af:STRING,revel:STRING,splice_ai_acceptor_gain_score:STRING,splice_ai_acceptor_gain_distance:STRING,splice_ai_acceptor_loss_score:STRING,splice_ai_acceptor_loss_distance:STRING,splice_ai_donor_gain_score:STRING,splice_ai_donor_gain_distance:STRING,splice_ai_donor_loss_score:STRING,splice_ai_donor_loss_distance:STRING,clinvar_classification:STRING,clinvar_last_updated:STRING,clinvar_phenotype:STRING,gnomad_all_af:STRING,gnomad_all_ac:STRING,gnomad_all_an:STRING,gnomad_max_af:STRING,gnomad_max_ac:STRING,gnomad_max_an:STRING,gnomad_max_subpop:STRING,gene_omim_id:STRING,omim_phenotypes_id:STRING,omim_phenotypes_name:STRING" File? gatk_override } @@ -305,7 +40,9 @@ workflow GvsSitesOnlyVCF { annotation_json = AnnotateVCF.annotation_json, annotation_json_jsi = AnnotateVCF.annotation_json_jsi, nirvana_schema = nirvana_schema, - project_id = project_id + project_id = project_id, + dataset_name = dataset_name + } } @@ -429,6 +166,7 @@ task BigQueryLoadJson { File annotation_json_jsi String nirvana_schema String project_id + String dataset_name } command <<< set -e From 7ee16b74c85ecbf1bfbdcf0d716ee7577b4a77f4 Mon Sep 17 00:00:00 2001 From: rori <6863459+RoriCremer@users.noreply.github.com> Date: Wed, 16 Jun 2021 02:13:27 -0400 Subject: [PATCH 14/73] add dataset param --- scripts/variantstore/wdl/GvsSitesOnlyVCF.example.inputs.json | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/scripts/variantstore/wdl/GvsSitesOnlyVCF.example.inputs.json b/scripts/variantstore/wdl/GvsSitesOnlyVCF.example.inputs.json index 1f717674da7..1bbd45f80b2 100644 --- a/scripts/variantstore/wdl/GvsSitesOnlyVCF.example.inputs.json +++ b/scripts/variantstore/wdl/GvsSitesOnlyVCF.example.inputs.json @@ -4,5 +4,7 @@ "GvsSitesOnlyVCF.output_merged_file_name": "hello_did_I_merge", "GvsSitesOnlyVCF.output_annotated_file_name": "hello_did_I_annotate", "GvsSitesOnlyVCF.nirvana_data_directory": "gs://broad-dsp-spec-ops/scratch/rcremer/Nirvana/NirvanaData.tar.gz", - "GvsSitesOnlyVCF.project_id": "spec-ops-aou" + "GvsSitesOnlyVCF.project_id": "spec-ops-aou", + "GvsSitesOnlyVCF.dataset_name": "anvil_100_for_testing" + } From ee59062122e6ef456085f36235d24cc38b7c2ebe Mon Sep 17 00:00:00 2001 From: rori <6863459+RoriCremer@users.noreply.github.com> Date: Thu, 17 Jun 2021 11:08:33 -0400 Subject: [PATCH 15/73] short term fix --- scripts/variantstore/wdl/GvsSitesOnlyVCF.wdl | 191 +++++++++++-------- 1 file changed, 112 insertions(+), 79 deletions(-) diff --git a/scripts/variantstore/wdl/GvsSitesOnlyVCF.wdl b/scripts/variantstore/wdl/GvsSitesOnlyVCF.wdl index 45dbd5b15b6..a2a16fc85d2 100644 --- a/scripts/variantstore/wdl/GvsSitesOnlyVCF.wdl +++ b/scripts/variantstore/wdl/GvsSitesOnlyVCF.wdl @@ -8,7 +8,7 @@ workflow GvsSitesOnlyVCF { String project_id String dataset_name File nirvana_data_directory - String nirvana_schema = "position:INTEGER,vid:String,contig:STRING,ref_allele:STRING,alt_allele:STRING,variant_type:STRING,genomic_location:STRING,dbsnp_rsid:STRING,transcript:STRING,gene_symbol:STRING,transcript_source:STRING,aa_change:STRING,consequence:STRING,dna_change:String,exon_number:STRING,intron_number:STRING,splice_distance:STRING,entrez_gene_id:STRING,is_canonical_transcript:STRING,gvs_all_ac:STRING,gvs_all_an:STRING,gvs_all_af:STRING,revel:STRING,splice_ai_acceptor_gain_score:STRING,splice_ai_acceptor_gain_distance:STRING,splice_ai_acceptor_loss_score:STRING,splice_ai_acceptor_loss_distance:STRING,splice_ai_donor_gain_score:STRING,splice_ai_donor_gain_distance:STRING,splice_ai_donor_loss_score:STRING,splice_ai_donor_loss_distance:STRING,clinvar_classification:STRING,clinvar_last_updated:STRING,clinvar_phenotype:STRING,gnomad_all_af:STRING,gnomad_all_ac:STRING,gnomad_all_an:STRING,gnomad_max_af:STRING,gnomad_max_ac:STRING,gnomad_max_an:STRING,gnomad_max_subpop:STRING,gene_omim_id:STRING,omim_phenotypes_id:STRING,omim_phenotypes_name:STRING" + String nirvana_schema = "position:INTEGER,vid:String,contig:STRING,ref_allele:STRING,alt_allele:STRING,variant_type:STRING,genomic_location:STRING,dbsnp_rsid:STRING,transcript:STRING,gene_symbol:STRING,transcript_source:STRING,aa_change:STRING,consequence:STRING,dna_change:String,exon_number:STRING,intron_number:STRING,splice_distance:STRING,entrez_gene_id:STRING,is_canonical_transcript:STRING,gvs_all_ac:INTEGER,gvs_all_an:INTEGER,gvs_all_af:INTEGER,revel:FLOAT,splice_ai_acceptor_gain_score:INTEGER,splice_ai_acceptor_gain_distance:INTEGER,splice_ai_acceptor_loss_score:INTEGER,splice_ai_acceptor_loss_distance:INTEGER,splice_ai_donor_gain_score:INTEGER,splice_ai_donor_gain_distance:INTEGER,splice_ai_donor_loss_score:INTEGER,splice_ai_donor_loss_distance:INTEGER,clinvar_classification:STRING,clinvar_last_updated:DATE,clinvar_phenotype:STRING,gnomad_all_af:STRING,gnomad_all_ac:STRING,gnomad_all_an:STRING,gnomad_max_af:STRING,gnomad_max_ac:STRING,gnomad_max_an:STRING,gnomad_max_subpop:STRING,gene_omim_id:STRING,omim_phenotypes_id:STRING,omim_phenotypes_name:STRING" File? gatk_override } @@ -35,14 +35,19 @@ workflow GvsSitesOnlyVCF { nirvana_data_tar = nirvana_data_directory } - call BigQueryLoadJson { + call PrepAnnotationJson { input: annotation_json = AnnotateVCF.annotation_json, - annotation_json_jsi = AnnotateVCF.annotation_json_jsi, + annotation_json_jsi = AnnotateVCF.annotation_json_jsi + + } + + call BigQueryLoadJson { + input: + annotation_json = PrepAnnotationJson.annotations_edited_file, nirvana_schema = nirvana_schema, project_id = project_id, dataset_name = dataset_name - } } @@ -160,104 +165,132 @@ task AnnotateVCF { } } -task BigQueryLoadJson { +task PrepAnnotationJson { input { File annotation_json File annotation_json_jsi - String nirvana_schema - String project_id - String dataset_name } + + String unzipped_json = "unzipped.json" + String newline_delimited_json = "load_into_bq.json" + command <<< set -e # prepare the json file for loading into BQ by making it a new line delimited json - jq -c '.positions | .[]' ~{annotation_json} > load_into_bq.json + gunzip -c ~{annotation_json} >> ~{unzipped_json} + jq -rc '.positions | .[]' ~{unzipped_json} >> ~{newline_delimited_json} - # load this json in as a temp interim BQ vat table - $TEMP_TABLE="~{dataset_name}.pre-vat" - bq --location=US load --project_id=~{project_id} --source_format=NEWLINE_DELIMITED_JSON --autodetect $TEMP_TABLE load_into_bq.json + >>> + # ------------------------------------------------ + # Runtime settings: + runtime { + docker: "stedolan/jq:latest" + memory: "3 GB" + cpu: "1" + disks: "local-disk 100 HDD" + } + # ------------------------------------------------ + # Outputs: + output { + File annotations_edited_file = newline_delimited_json + } +} +task BigQueryLoadJson { + input { + File annotation_json + String nirvana_schema + String project_id + String dataset_name + } - # make the BQ vat table (this will help with validation) + command <<< + set -e + + # load the annotation json in as a temp interim BQ vat table + TEMP_TABLE="~{dataset_name}.pre-vat" + bq --location=US load --project_id=~{project_id} --source_format=NEWLINE_DELIMITED_JSON --autodetect $TEMP_TABLE ~{annotation_json} + + # create the final vat table with the correct fields + # TODO this is a hacky set of fields---would ideally use the vat_schema.json PARTITION_FIELD="position" CLUSTERING_FIELD="vid" - PARTITION_STRING="--range_partitioning=$PARTITION_FIELD,0,4000,4000" - CLUSTERING_STRING="--clustering_fields=$CLUSTERING_FIELD" + PARTITION_STRING="" #--range_partitioning=$PARTITION_FIELD,0,4000,4000" + CLUSTERING_STRING="" #--clustering_fields=$CLUSTERING_FIELD" TABLE="~{dataset_name}.vatter" SCHEMA="~{nirvana_schema}" PROJECT="~{project_id}" - - # bq --location=US mk --project_id="spec-ops-aou" "anvil_100_for_testing.vat" "scripts/variantstore/wdl/schemas/vat_schema.json" + echo "Creating a vat table..." bq --location=US mk ${PARTITION_STRING} ${CLUSTERING_STRING} --project_id=~{project_id} $TABLE $SCHEMA > status_bq_submission + echo "And putting data into it" # now run some giant query in BQ to get this all in the right table - bq query --destination_table=$TABLE \ - 'SELECT - v.position, - v.vid, - v.chromosome AS contig, - v.refAllele AS ref_allele, - v.altAllele AS alt_allele, - v.variantType AS variant_type, - v.hgvsg AS genomic_location, - v.dbsnp AS dbsnp_rsid, - t.transcript, - t.hgnc AS gene_symbol, - t.source AS transcript_source, - t.hgvsp AS aa_change, - t.consequence as consequence, # gross, - t.hgvsc AS dna_change, - t.exons AS exon_number, - t.introns AS intron_number, - t.hgvsc AS splice_distance, - t.geneId AS entrez_gene_id, - CASE WHEN ( v.transcript is not null and t.isCanonical is not True) THEN False WHEN ( v.transcript is not null and t.isCanonical is True) THEN True END AS is_canonical_transcript, - null AS gvs_all_ac, # what is this mapping? - null AS gvs_all_an, - null AS gvs_all_af, - v.revel.score AS revel, - # we just grab the first value in spliceAI (need to validate that there will only ever be one) - CASE WHEN (select array_length(v.spliceAI)) > 0 - THEN v.spliceAI[offset(0)].acceptorGainScore END AS splice_ai_acceptor_gain_score, - CASE WHEN (select array_length(v.spliceAI)) > 0 - THEN v.spliceAI[offset(0)].acceptorGainDistance END AS splice_ai_acceptor_gain_distance, - CASE WHEN (select array_length(v.spliceAI)) > 0 - THEN v.spliceAI[offset(0)].acceptorLossScore END AS splice_ai_acceptor_loss_score, - CASE WHEN (select array_length(v.spliceAI)) > 0 - THEN v.spliceAI[offset(0)].acceptorLossDistance END AS splice_ai_acceptor_loss_distance, - CASE WHEN (select array_length(v.spliceAI)) > 0 - THEN v.spliceAI[offset(0)].donorGainScore END AS splice_ai_donor_gain_score, - CASE WHEN (select array_length(v.spliceAI)) > 0 - THEN v.spliceAI[offset(0)].donorGainDistance END AS splice_ai_donor_gain_distance, - CASE WHEN (select array_length(v.spliceAI)) > 0 - THEN v.spliceAI[offset(0)].donorLossScore END AS splice_ai_donor_loss_score, - CASE WHEN (select array_length(v.spliceAI)) > 0 - THEN v.spliceAI[offset(0)].donorLossDistance END AS splice_ai_donor_loss_distance, - (SELECT significance[offset(0)] FROM v.clinvar WHERE id LIKE "RCV%") AS clinvar_classification, - (SELECT lastUpdatedDate FROM v.clinvar WHERE id LIKE "RCV%") AS clinvar_last_updated, - (SELECT phenotypes FROM v.clinvar WHERE id LIKE "RCV%") AS clinvar_phenotype, - v.gnomad.allAf AS gnomad_all_af, - v.gnomad.allAc AS gnomad_all_ac, - v.gnomad.allAn AS gnomad_all_an, - v.gnomad.afrAf AS gnomad_max_af, - v.gnomad.afrAc AS gnomad_max_ac, - v.gnomad.afrAn AS gnomad_max_an, - null AS gnomad_max_subpop, # what is this mapping? - null AS gene_omim_id, - null AS omim_phenotypes_id, - null AS omim_phenotypes_name, - from (SELECT position, variantline.* FROM $PROJECT.$TABLE, UNNEST(variants) as variantline) as a left join - (SELECT position, variantline.vid, transcriptline.* FROM $PROJECT.$TABLE, UNNEST(variants) as variantline, UNNEST(variantline.transcripts) as transcriptline) as b on a.vid = b.vid)' + bq query --destination_table="anvil_100_for_testing.vatter" --project_id="spec-ops-aou" 'SELECT + v.position, + v.vid, + v.chromosome AS contig, + v.refAllele AS ref_allele, + v.altAllele AS alt_allele, + v.variantType AS variant_type, + v.hgvsg AS genomic_location, + ARRAY_TO_STRING(v.dbsnp, ",") AS dbsnp_rsid, + t.transcript, + t.hgnc AS gene_symbol, + t.source AS transcript_source, + t.hgvsp AS aa_change, + ARRAY_TO_STRING(t.consequence, ",") AS consequence, + t.hgvsc AS dna_change, + t.exons AS exon_number, + t.introns AS intron_number, + t.hgvsc AS splice_distance, + t.geneId AS entrez_gene_id, + CASE WHEN ( t.transcript is not null and t.isCanonical is not True) THEN "false" WHEN ( t.transcript is not null and t.isCanonical is True) THEN "true" END AS is_canonical_transcript, + null AS gvs_all_ac, + null AS gvs_all_an, + null AS gvs_all_af, + v.revel.score AS revel, + # we just grab the first value in spliceAI (need to validate that there will only ever be one) + CASE WHEN (select array_length(v.spliceAI)) > 0 + THEN v.spliceAI[offset(0)].acceptorGainScore END AS splice_ai_acceptor_gain_score, + CASE WHEN (select array_length(v.spliceAI)) > 0 + THEN v.spliceAI[offset(0)].acceptorGainDistance END AS splice_ai_acceptor_gain_distance, + CASE WHEN (select array_length(v.spliceAI)) > 0 + THEN v.spliceAI[offset(0)].acceptorLossScore END AS splice_ai_acceptor_loss_score, + CASE WHEN (select array_length(v.spliceAI)) > 0 + THEN v.spliceAI[offset(0)].acceptorLossDistance END AS splice_ai_acceptor_loss_distance, + CASE WHEN (select array_length(v.spliceAI)) > 0 + THEN v.spliceAI[offset(0)].donorGainScore END AS splice_ai_donor_gain_score, + CASE WHEN (select array_length(v.spliceAI)) > 0 + THEN v.spliceAI[offset(0)].donorGainDistance END AS splice_ai_donor_gain_distance, + CASE WHEN (select array_length(v.spliceAI)) > 0 + THEN v.spliceAI[offset(0)].donorLossScore END AS splice_ai_donor_loss_score, + CASE WHEN (select array_length(v.spliceAI)) > 0 + THEN v.spliceAI[offset(0)].donorLossDistance END AS splice_ai_donor_loss_distance, + (SELECT ARRAY_TO_STRING(significance, ",") FROM v.clinvar WHERE id LIKE "RCV%") AS clinvar_classification, + (SELECT lastUpdatedDate FROM v.clinvar WHERE id LIKE "RCV%") AS clinvar_last_updated, + (SELECT ARRAY_TO_STRING(phenotypes, ",") FROM v.clinvar WHERE id LIKE "RCV%") AS clinvar_phenotype, + v.gnomad.allAf AS gnomad_all_af, + v.gnomad.allAc AS gnomad_all_ac, + v.gnomad.allAn AS gnomad_all_an, + v.gnomad.afrAf AS gnomad_max_af, + v.gnomad.afrAc AS gnomad_max_ac, + v.gnomad.afrAn AS gnomad_max_an, + null AS gnomad_max_subpop, # what is this mapping? + null AS gene_omim_id, + null AS omim_phenotypes_id, + null AS omim_phenotypes_name, + from (SELECT position, variantline.* FROM `spec-ops-aou.anvil_100_for_testing.pre-vat`, UNNEST(variants) as variantline) as v left join + (SELECT position, variantline.vid, transcriptline.* FROM `spec-ops-aou.anvil_100_for_testing.pre-vat`, UNNEST(variants) as variantline, UNNEST(variantline.transcripts) as transcriptline) as t on v.vid = t.vid' + # cat status_bq_submission | tail -n 1 > status_bq_submission_last_line + # bq_job_id=$(sed 's/.*://' status_bq_submission_last_line) + #echo $bq_job_id - cat status_bq_submission | tail -n 1 > status_bq_submission_last_line - bq_job_id=$(sed 's/.*://' status_bq_submission_last_line) - echo $bq_job_id >>> # ------------------------------------------------ # Runtime settings: runtime { - docker: "broadinstitute/gatk:4.2.0.0" + docker: "openbridge/ob_google-bigquery:latest" memory: "3 GB" cpu: "1" disks: "local-disk 100 HDD" @@ -265,7 +298,7 @@ task BigQueryLoadJson { # ------------------------------------------------ # Outputs: output { - Boolean done = true + Boolean done = true } } From bbcf684830877a87af4b56ddb67d5288df72c653 Mon Sep 17 00:00:00 2001 From: rori <6863459+RoriCremer@users.noreply.github.com> Date: Tue, 22 Jun 2021 00:30:14 -0400 Subject: [PATCH 16/73] update for nirvana results? --- .../variantstore/wdl/schemas/vat_schema.json | 40 +++++++++---------- 1 file changed, 20 insertions(+), 20 deletions(-) diff --git a/scripts/variantstore/wdl/schemas/vat_schema.json b/scripts/variantstore/wdl/schemas/vat_schema.json index aa3fe6b7cde..29481214de4 100644 --- a/scripts/variantstore/wdl/schemas/vat_schema.json +++ b/scripts/variantstore/wdl/schemas/vat_schema.json @@ -114,9 +114,9 @@ "mode": "Nullable" }, { - "description": "AC TODO -- this needs to be added back and swapped to required", + "description": "AC TODO -- this needs to be added back and swapped to required -- Lee said this was a string?", "name": "gvs_all_ac", - "type": "String", + "type": "Integer", "mode": "Nullable" }, { @@ -126,21 +126,21 @@ "mode": "Nullable" }, { - "description": "AF TODO -- this needs to be added back and swapped to required", + "description": "AF TODO -- this needs to be added back and swapped to required -- Lee said this was a Float?", "name": "gvs_all_af", - "type": "Float", + "type": "INTEGER", "mode": "Nullable" }, { - "description": "REVEL", + "description": "REVEL -- Lee said this was a string?", "name": "revel", - "type": "String", + "type": "FLOAT", "mode": "Nullable" }, { - "description": "Slice AI", + "description": "Slice AI -- Lee said this was a Float?", "name": "splice_ai_acceptor_gain_score", - "type": "Float", + "type": "Integer", "mode": "Nullable" }, { @@ -150,9 +150,9 @@ "mode": "Nullable" }, { - "description": "Slice AI", + "description": "Slice AI -- Lee said this was a Float?", "name": "splice_ai_acceptor_loss_score", - "type": "Float", + "type": "Integer", "mode": "Nullable" }, { @@ -162,9 +162,9 @@ "mode": "Nullable" }, { - "description": "Slice AI", + "description": "Slice AI -- Lee said this was a Float?", "name": "splice_ai_donor_gain_score", - "type": "Float", + "type": "Integer", "mode": "Nullable" }, { @@ -174,9 +174,9 @@ "mode": "Nullable" }, { - "description": "Slice AI", + "description": "Slice AI -- Lee said this was a Float?", "name": "splice_ai_donor_loss_score", - "type": "Float", + "type": "Integer", "mode": "Nullable" }, { @@ -198,10 +198,10 @@ "mode": "Nullable" }, { - "description": "ClinVar Disease Name", + "description": "ClinVar Disease Name TODO Repeated", "name": "clinvar_phenotype", "type": "String", - "mode": "Repeated" + "mode": "Nullable" }, { "description": "gnomAD: 'Total' frequency", @@ -240,9 +240,9 @@ "mode": "Nullable" }, { - "description": "gnomAD: Max subpopulation ethnicity", + "description": "gnomAD: Max subpopulation ethnicity -- TODO this should be a string but I need a value first. Hey Lee, I need a mapping!", "name": "gnomad_max_subpop", - "type": "String", + "type": "INTEGER", "mode": "Nullable" }, { @@ -258,9 +258,9 @@ "mode": "Nullable" }, { - "description": "OMIM Disease Name TODO -- this needs to be swapped to Repeated not nullable", + "description": "OMIM Disease Name TODO -- this needs to be swapped to Repeated not nullable and String not Integer?", "name": "omim_phenotypes_name", - "type": "String", + "type": "Integer", "mode": "Nullable" } ] From 5b510f7b40be7fa25b951093559f2d87eb2d39c6 Mon Sep 17 00:00:00 2001 From: rori <6863459+RoriCremer@users.noreply.github.com> Date: Wed, 23 Jun 2021 11:23:54 -0400 Subject: [PATCH 17/73] remove test files --- hello_did_I_annotate_testt.json | 299 -------------------------------- 1 file changed, 299 deletions(-) delete mode 100644 hello_did_I_annotate_testt.json diff --git a/hello_did_I_annotate_testt.json b/hello_did_I_annotate_testt.json deleted file mode 100644 index 13f2922e001..00000000000 --- a/hello_did_I_annotate_testt.json +++ /dev/null @@ -1,299 +0,0 @@ -{"header":{"annotator":"Nirvana 3.13.0","creationTime":"2021-06-12 01:47:58","genomeAssembly":"GRCh38","schemaVersion":6,"dataVersion":"91.27.61","dataSources":[{"name":"VEP","version":"91","description":"BothRefSeqAndEnsembl","releaseDate":"2017-12-18"},{"name":"MultiZ100Way","version":"20171006","description":"Amino acid conservation scores calculated from MultiZ100Way alignments from UCSC.","releaseDate":"2017-10-06"},{"name":"ClinVar","version":"20200903","description":"A freely accessible, public archive of reports of the relationships among human variations and phenotypes, with supporting evidence","releaseDate":"2020-09-03"},{"name":"dbSNP","version":"154","description":"Identifiers for observed variants","releaseDate":"2020-05-01"},{"name":"dbSNP","version":"151","description":"Identifiers for observed variants","releaseDate":"2018-04-18"},{"name":"gnomAD","version":"2.1","description":"gnomAD allele frequency data remapped to GRCh38 with CrossMap by Ensembl","releaseDate":"2019-03-25"},{"name":"MITOMAP","version":"20200819","description":"Small variants in the MITOMAP human mitochondrial genome database","releaseDate":"2020-08-19"},{"name":"1000 Genomes Project","version":"Phase 3 v3plus","description":"A public catalogue of human variation and genotype data","releaseDate":"2013-05-27"},{"name":"PrimateAI","version":"0.2","description":"PrimateAI percentile scores.","releaseDate":"2018-11-07"},{"name":"REVEL","version":"20200205","description":"Pathogenicity scores of missense variants predicted by REVEL","releaseDate":"2020-02-05"},{"name":"SpliceAI","version":"1.3","description":"SpliceAI scores, distances, etc.","releaseDate":"2019-10-04"},{"name":"TOPMed","version":"freeze_5","description":"Allele frequencies from TOPMed data","releaseDate":"2017-08-28"},{"name":"ClinGen","version":"20160414","releaseDate":"2016-04-14"},{"name":"ClinGen Dosage Sensitivity 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-{"chromosome":"chr20","position":198921,"refAllele":"A","altAlleles":["G"],"cytogeneticBand":"20p13","variants":[{"vid":"20-198921-A-G","chromosome":"chr20","begin":198921,"end":198921,"refAllele":"A","altAllele":"G","variantType":"SNV","hgvsg":"NC_000020.11:g.198921A>G","phylopScore":-2.1,"dbsnp":["rs6033277"],"globalAllele":{"globalMinorAllele":"A","globalMinorAlleleFrequency":0.4696},"gnomad":{"coverage":19,"allAf":0.508515,"allAn":31240,"allAc":15886,"allHc":3999,"afrAf":0.511427,"afrAn":8664,"afrAc":4431,"afrHc":1080,"amrAf":0.477435,"amrAn":842,"amrAc":402,"amrHc":96,"easAf":0.500645,"easAn":1550,"easAc":776,"easHc":191,"finAf":0.494804,"finAn":3464,"finAc":1714,"finHc":439,"nfeAf":0.513748,"nfeAn":15348,"nfeAc":7885,"nfeHc":2027,"asjAf":0.47931,"asjAn":290,"asjAc":139,"asjHc":31,"othAf":0.498152,"othAn":1082,"othAc":539,"othHc":135,"maleAf":0.508913,"maleAn":17390,"maleAc":8850,"maleHc":2200,"femaleAf":0.508014,"femaleAn":13850,"femaleAc":7036,"femaleHc":1799,"controlsAllAf":0.510287,"controlsAllAn":10790,"controlsAllAc":5506},"oneKg":{"allAf":0.530351,"afrAf":0.520424,"amrAf":0.482709,"easAf":0.566468,"eurAf":0.478131,"sasAf":0.59407,"allAn":5008,"afrAn":1322,"amrAn":694,"easAn":1008,"eurAn":1006,"sasAn":978,"allAc":2656,"afrAc":688,"amrAc":335,"easAc":571,"eurAc":481,"sasAc":581},"topmed":{"allAf":0.507725,"allAn":125568,"allAc":63754,"allHc":16184}}]}, -{"chromosome":"chr20","position":199094,"refAllele":"TTAAAA","altAlleles":["T"],"cytogeneticBand":"20p13","variants":[{"vid":"20-199094-TTAAAA-T","chromosome":"chr20","begin":199095,"end":199099,"refAllele":"TAAAA","altAllele":"-","variantType":"deletion","hgvsg":"NC_000020.11:g.199100_199104del","dbsnp":["rs76051089"],"gnomad":{"coverage":17,"allAf":0.143474,"allAn":28932,"allAc":4151,"allHc":385,"afrAf":0.05794,"afrAn":8388,"afrAc":486,"afrHc":12,"amrAf":0.127005,"amrAn":748,"amrAc":95,"amrHc":8,"easAf":0.085286,"easAn":1536,"easAc":131,"easHc":4,"finAf":0.169538,"finAn":2554,"finAc":433,"finHc":47,"nfeAf":0.193446,"nfeAn":14464,"nfeAc":2798,"nfeHc":296,"asjAf":0.163121,"asjAn":282,"asjAc":46,"asjHc":4,"othAf":0.16875,"othAn":960,"othAc":162,"othHc":14,"maleAf":0.143412,"maleAn":16212,"maleAc":2325,"maleHc":212,"femaleAf":0.143553,"femaleAn":12720,"femaleAc":1826,"femaleHc":173,"controlsAllAf":0.137913,"controlsAllAn":9448,"controlsAllAc":1303},"oneKg":{"allAf":0.096446,"afrAf":0.024206,"amrAf":0.123919,"easAf":0.064484,"eurAf":0.229622,"sasAf":0.070552,"allAn":5008,"afrAn":1322,"amrAn":694,"easAn":1008,"eurAn":1006,"sasAn":978,"allAc":483,"afrAc":32,"amrAc":86,"easAc":65,"eurAc":231,"sasAc":69},"topmed":{"allAf":0.148398,"allAn":125568,"allAc":18634,"allHc":1612,"failedFilter":true}}]}, -{"chromosome":"chr20","position":199123,"refAllele":"T","altAlleles":["C"],"cytogeneticBand":"20p13","variants":[{"vid":"20-199123-T-C","chromosome":"chr20","begin":199123,"end":199123,"refAllele":"T","altAllele":"C","variantType":"SNV","hgvsg":"NC_000020.11:g.199123T>C","phylopScore":0.2,"dbsnp":["rs1946670"],"globalAllele":{"globalMinorAllele":"C","globalMinorAlleleFrequency":0.3774},"gnomad":{"coverage":16,"allAf":0.323628,"allAn":27374,"allAc":8859,"allHc":1729,"afrAf":0.166829,"afrAn":8194,"afrAc":1367,"afrHc":116,"amrAf":0.357784,"amrAn":668,"amrAc":239,"amrHc":49,"easAf":0.487871,"easAn":1484,"easAc":724,"easHc":174,"finAf":0.362152,"finAn":2082,"finAc":754,"finHc":182,"nfeAf":0.388041,"nfeAn":13764,"nfeAc":5341,"nfeHc":1122,"asjAf":0.345324,"asjAn":278,"asjAc":96,"asjHc":18,"othAf":0.373894,"othAn":904,"othAc":338,"othHc":68,"maleAf":0.325566,"maleAn":15450,"maleAc":5030,"maleHc":980,"femaleAf":0.321117,"femaleAn":11924,"femaleAc":3829,"femaleHc":749,"controlsAllAf":0.328082,"controlsAllAn":8632,"controlsAllAc":2832},"oneKg":{"allAf":0.377396,"afrAf":0.155068,"amrAf":0.402017,"easAf":0.556548,"eurAf":0.387674,"sasAf":0.465235,"allAn":5008,"afrAn":1322,"amrAn":694,"easAn":1008,"eurAn":1006,"sasAn":978,"allAc":1890,"afrAc":205,"amrAc":279,"easAc":561,"eurAc":390,"sasAc":455},"topmed":{"allAf":0.33769,"allAn":125568,"allAc":42403,"allHc":7982}}]}, -{"chromosome":"chr20","position":199139,"refAllele":"C","altAlleles":["CTT"],"cytogeneticBand":"20p13","variants":[{"vid":"20-199139-C-CTT","chromosome":"chr20","begin":199140,"end":199139,"refAllele":"-","altAllele":"TT","variantType":"insertion","hgvsg":"NC_000020.11:g.199161_199162dupTT","inLowComplexityRegion":true,"dbsnp":["rs1160950757"],"topmed":{"allAf":0.279339,"allAn":125568,"allAc":35076,"allHc":2288,"failedFilter":true}}]} -],"genes":[ -{"name":"DEFB126","gnomAD":{"pLi":4.08e-1,"pRec":4.78e-1,"pNull":1.14e-1,"synZ":-7.40e-1,"misZ":-2.62e-1,"loeuf":1.68e0}}, -{"name":"DEFB127","gnomAD":{"pLi":4.05e-1,"pRec":4.79e-1,"pNull":1.16e-1,"synZ":-2.93e-1,"misZ":-1.48e-1,"loeuf":1.69e0}}, -{"name":"DEFB128","gnomAD":{"pLi":3.96e-1,"pRec":4.82e-1,"pNull":1.22e-1,"synZ":-1.87e0,"misZ":-8.54e-1,"loeuf":1.72e0}} -]} From 39df10865a424b95862bebb5f2c827775db46da5 Mon Sep 17 00:00:00 2001 From: rori <6863459+RoriCremer@users.noreply.github.com> Date: Wed, 23 Jun 2021 11:25:22 -0400 Subject: [PATCH 18/73] schema update --- scripts/variantstore/wdl/schemas/vat_schema.json | 16 ++++++++-------- 1 file changed, 8 insertions(+), 8 deletions(-) diff --git a/scripts/variantstore/wdl/schemas/vat_schema.json b/scripts/variantstore/wdl/schemas/vat_schema.json index 29481214de4..ba1fbac2a21 100644 --- a/scripts/variantstore/wdl/schemas/vat_schema.json +++ b/scripts/variantstore/wdl/schemas/vat_schema.json @@ -138,9 +138,9 @@ "mode": "Nullable" }, { - "description": "Slice AI -- Lee said this was a Float?", + "description": "Slice AI", "name": "splice_ai_acceptor_gain_score", - "type": "Integer", + "type": "Float", "mode": "Nullable" }, { @@ -150,9 +150,9 @@ "mode": "Nullable" }, { - "description": "Slice AI -- Lee said this was a Float?", + "description": "Slice AI", "name": "splice_ai_acceptor_loss_score", - "type": "Integer", + "type": "Float", "mode": "Nullable" }, { @@ -162,9 +162,9 @@ "mode": "Nullable" }, { - "description": "Slice AI -- Lee said this was a Float?", + "description": "Slice AI", "name": "splice_ai_donor_gain_score", - "type": "Integer", + "type": "Float", "mode": "Nullable" }, { @@ -174,9 +174,9 @@ "mode": "Nullable" }, { - "description": "Slice AI -- Lee said this was a Float?", + "description": "Slice AI", "name": "splice_ai_donor_loss_score", - "type": "Integer", + "type": "Float", "mode": "Nullable" }, { From 47cf857112870924e09241878d6379396bfc10fe Mon Sep 17 00:00:00 2001 From: rori <6863459+RoriCremer@users.noreply.github.com> Date: Wed, 23 Jun 2021 12:04:14 -0400 Subject: [PATCH 19/73] omg so many vcfs! --- scripts/variantstore/wdl/GvsSitesOnlyVCF.example.inputs.json | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/scripts/variantstore/wdl/GvsSitesOnlyVCF.example.inputs.json b/scripts/variantstore/wdl/GvsSitesOnlyVCF.example.inputs.json index 1bbd45f80b2..d8101d0f26e 100644 --- a/scripts/variantstore/wdl/GvsSitesOnlyVCF.example.inputs.json +++ b/scripts/variantstore/wdl/GvsSitesOnlyVCF.example.inputs.json @@ -1,10 +1,11 @@ { - "GvsSitesOnlyVCF.gvs_extract_cohort_filtered_vcfs": ["gs://broad-dsp-spec-ops/scratch/rcremer/Nirvana/Data/anvil_expected.vcf"], + "GvsSitesOnlyVCF.gvs_extract_cohort_filtered_vcfs": ["gs://broad-dsp-spec-ops/kcibul/ft/gvs.chr20.vcf.gz", "gs://broad-dsp-spec-ops/scratch/rcremer/Nirvana/Data/gvs_features_0.vcf.gz"], + "GvsSitesOnlyVCF.gvs_extract_cohort_filtered_vcf_indices": ["gs://broad-dsp-spec-ops/kcibul/ft/gvs.chr20.vcf.gz.tbi", "gs://broad-dsp-spec-ops/scratch/rcremer/Nirvana/Data/gvs_features_0.vcf.gz.tbi"], "GvsSitesOnlyVCF.output_sites_only_file_name": "hello_did_I_sites_only", "GvsSitesOnlyVCF.output_merged_file_name": "hello_did_I_merge", "GvsSitesOnlyVCF.output_annotated_file_name": "hello_did_I_annotate", "GvsSitesOnlyVCF.nirvana_data_directory": "gs://broad-dsp-spec-ops/scratch/rcremer/Nirvana/NirvanaData.tar.gz", + "GvsSitesOnlyVCF.nirvana_schema_json_file": "gs://broad-dsp-spec-ops/scratch/rcremer/Nirvana/schemas/vat_schema.json", "GvsSitesOnlyVCF.project_id": "spec-ops-aou", "GvsSitesOnlyVCF.dataset_name": "anvil_100_for_testing" - } From efb488a083a91f0d828bd904e7cbe7d23cce8395 Mon Sep 17 00:00:00 2001 From: rori <6863459+RoriCremer@users.noreply.github.com> Date: Wed, 23 Jun 2021 12:24:30 -0400 Subject: [PATCH 20/73] genes schema for a join later on --- .../wdl/schemas/vat_genes_schema.json | 20 +++++++++++++++++++ 1 file changed, 20 insertions(+) create mode 100644 scripts/variantstore/wdl/schemas/vat_genes_schema.json diff --git a/scripts/variantstore/wdl/schemas/vat_genes_schema.json b/scripts/variantstore/wdl/schemas/vat_genes_schema.json new file mode 100644 index 00000000000..6ad699c01bb --- /dev/null +++ b/scripts/variantstore/wdl/schemas/vat_genes_schema.json @@ -0,0 +1,20 @@ +[ +{ +"description": "OMIM ID", +"name": "gene_omim_id", +"type": "Integer", +"mode": "Nullable" +}, +{ +"description": "OMIM Disease ID TODO -- this needs to be swapped to Repeated not nullable", +"name": "omim_phenotypes_id", +"type": "Integer", +"mode": "Nullable" +}, +{ +"description": "OMIM Disease Name TODO -- this needs to be swapped to Repeated not nullable and String not Integer?", +"name": "omim_phenotypes_name", +"type": "Integer", +"mode": "Nullable" +} +] \ No newline at end of file From 7de95315308a53fd001eb6a977391c35ac440331 Mon Sep 17 00:00:00 2001 From: rori <6863459+RoriCremer@users.noreply.github.com> Date: Wed, 23 Jun 2021 12:24:59 -0400 Subject: [PATCH 21/73] this vat schema works for the csv upload --- .../variantstore/wdl/schemas/vat_schema.json | 18 ------------------ 1 file changed, 18 deletions(-) diff --git a/scripts/variantstore/wdl/schemas/vat_schema.json b/scripts/variantstore/wdl/schemas/vat_schema.json index ba1fbac2a21..f281fb0f2ec 100644 --- a/scripts/variantstore/wdl/schemas/vat_schema.json +++ b/scripts/variantstore/wdl/schemas/vat_schema.json @@ -244,23 +244,5 @@ "name": "gnomad_max_subpop", "type": "INTEGER", "mode": "Nullable" - }, - { - "description": "OMIM ID", - "name": "gene_omim_id", - "type": "Integer", - "mode": "Nullable" - }, - { - "description": "OMIM Disease ID TODO -- this needs to be swapped to Repeated not nullable", - "name": "omim_phenotypes_id", - "type": "Integer", - "mode": "Nullable" - }, - { - "description": "OMIM Disease Name TODO -- this needs to be swapped to Repeated not nullable and String not Integer?", - "name": "omim_phenotypes_name", - "type": "Integer", - "mode": "Nullable" } ] From aca070da951aeb8521857a79e9db713b042ae8f1 Mon Sep 17 00:00:00 2001 From: rori <6863459+RoriCremer@users.noreply.github.com> Date: Wed, 23 Jun 2021 19:13:37 -0400 Subject: [PATCH 22/73] schema update --- scripts/variantstore/wdl/schemas/vat_schema.json | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/scripts/variantstore/wdl/schemas/vat_schema.json b/scripts/variantstore/wdl/schemas/vat_schema.json index f281fb0f2ec..8730d52dc2a 100644 --- a/scripts/variantstore/wdl/schemas/vat_schema.json +++ b/scripts/variantstore/wdl/schemas/vat_schema.json @@ -132,7 +132,7 @@ "mode": "Nullable" }, { - "description": "REVEL -- Lee said this was a string?", + "description": "REVEL", "name": "revel", "type": "FLOAT", "mode": "Nullable" From b350152aecdc3a3f22cb2e01adc863cae1db91f8 Mon Sep 17 00:00:00 2001 From: rori <6863459+RoriCremer@users.noreply.github.com> Date: Wed, 23 Jun 2021 19:13:52 -0400 Subject: [PATCH 23/73] genes table schema --- scripts/variantstore/wdl/schemas/vat_genes_schema.json | 6 ++++++ 1 file changed, 6 insertions(+) diff --git a/scripts/variantstore/wdl/schemas/vat_genes_schema.json b/scripts/variantstore/wdl/schemas/vat_genes_schema.json index 6ad699c01bb..bdefadf854d 100644 --- a/scripts/variantstore/wdl/schemas/vat_genes_schema.json +++ b/scripts/variantstore/wdl/schemas/vat_genes_schema.json @@ -1,4 +1,10 @@ [ + { + "description": "gene name", + "name": "gene_symbol", + "type": "String", + "mode": "Nullable" + }, { "description": "OMIM ID", "name": "gene_omim_id", From b9ce0cd2dd2d526405898bf9b377c52ec97a07c7 Mon Sep 17 00:00:00 2001 From: rori <6863459+RoriCremer@users.noreply.github.com> Date: Wed, 23 Jun 2021 19:14:12 -0400 Subject: [PATCH 24/73] more wdl drama --- scripts/variantstore/wdl/GvsSitesOnlyVCF.wdl | 177 ++++++++++++------- 1 file changed, 114 insertions(+), 63 deletions(-) diff --git a/scripts/variantstore/wdl/GvsSitesOnlyVCF.wdl b/scripts/variantstore/wdl/GvsSitesOnlyVCF.wdl index a2a16fc85d2..eb30502f30d 100644 --- a/scripts/variantstore/wdl/GvsSitesOnlyVCF.wdl +++ b/scripts/variantstore/wdl/GvsSitesOnlyVCF.wdl @@ -1,22 +1,25 @@ version 1.0 -workflow GvsSitesOnlyVCF { +workflow GvsSitesOnlyVCF { # tested with "gs://broad-dsp-spec-ops/scratch/rcremer/Nirvana/Data/anvil_expected.vcf" input { - Array[File] gvs_extract_cohort_filtered_vcfs + Array[File] gvs_extract_cohort_filtered_vcfs # gonna try this one next: gs://broad-dsp-spec-ops/kcibul/ft/gvs.chr20.vcf.gz, + Array[File] gvs_extract_cohort_filtered_vcf_indices # gonna try this one next: gs://broad-dsp-spec-ops/kcibul/ft/gvs.chr20.vcf.gz, String output_sites_only_file_name String output_merged_file_name String output_annotated_file_name String project_id String dataset_name File nirvana_data_directory - String nirvana_schema = "position:INTEGER,vid:String,contig:STRING,ref_allele:STRING,alt_allele:STRING,variant_type:STRING,genomic_location:STRING,dbsnp_rsid:STRING,transcript:STRING,gene_symbol:STRING,transcript_source:STRING,aa_change:STRING,consequence:STRING,dna_change:String,exon_number:STRING,intron_number:STRING,splice_distance:STRING,entrez_gene_id:STRING,is_canonical_transcript:STRING,gvs_all_ac:INTEGER,gvs_all_an:INTEGER,gvs_all_af:INTEGER,revel:FLOAT,splice_ai_acceptor_gain_score:INTEGER,splice_ai_acceptor_gain_distance:INTEGER,splice_ai_acceptor_loss_score:INTEGER,splice_ai_acceptor_loss_distance:INTEGER,splice_ai_donor_gain_score:INTEGER,splice_ai_donor_gain_distance:INTEGER,splice_ai_donor_loss_score:INTEGER,splice_ai_donor_loss_distance:INTEGER,clinvar_classification:STRING,clinvar_last_updated:DATE,clinvar_phenotype:STRING,gnomad_all_af:STRING,gnomad_all_ac:STRING,gnomad_all_an:STRING,gnomad_max_af:STRING,gnomad_max_ac:STRING,gnomad_max_an:STRING,gnomad_max_subpop:STRING,gene_omim_id:STRING,omim_phenotypes_id:STRING,omim_phenotypes_name:STRING" + File nirvana_schema_json_file + String? genes_vat_schema = "gene_symbol:STRING,gene_omim_id:INTEGER,omim_phenotypes_id:INTEGER,omim_phenotypes_name:STRING" File? gatk_override } scatter(i in range(length(gvs_extract_cohort_filtered_vcfs)) ) { call SitesOnlyVcf { input: - vcf_bgz_gts = gvs_extract_cohort_filtered_vcfs[i], - output_filename = "${output_sites_only_file_name}_${i}.sites_only.vcf.gz", + vcf_bgz_gts = gvs_extract_cohort_filtered_vcfs[i], + vcf_index = gvs_extract_cohort_filtered_vcf_indices[i], + output_filename = "${output_sites_only_file_name}_${i}.sites_only.vcf.gz", } } @@ -34,21 +37,26 @@ workflow GvsSitesOnlyVCF { output_annotated_file_name = output_annotated_file_name, nirvana_data_tar = nirvana_data_directory } + #call AnnotateShardedVCF { + # input: + # input_vcfs = SitesOnlyVcf.output_vcf, + # output_annotated_file_name = output_annotated_file_name, + # nirvana_data_tar = nirvana_data_directory + #} - call PrepAnnotationJson { - input: - annotation_json = AnnotateVCF.annotation_json, - annotation_json_jsi = AnnotateVCF.annotation_json_jsi - - } + # call PrepAnnotationJson { # prep w a python script-- we are assuming BQ docker has python? + # input: + # annotation_json = AnnotateVCF.annotation_json, + # } - call BigQueryLoadJson { - input: - annotation_json = PrepAnnotationJson.annotations_edited_file, - nirvana_schema = nirvana_schema, - project_id = project_id, - dataset_name = dataset_name - } + # call BigQueryLoadJson { + # input: + # annotation_json = AnnotateVCF.annotation_json, + # #annotation_json_jsi = AnnotateVCF.annotation_json_jsi + # nirvana_schema = nirvana_schema_json_file, + # project_id = project_id, + # dataset_name = dataset_name + # } } @@ -57,9 +65,10 @@ workflow GvsSitesOnlyVCF { task SitesOnlyVcf { input { File vcf_bgz_gts + File vcf_index String output_filename } - String output_vcf_idx = basename(output_filename) + ".tbi" # or will this be .idx if from .vcf.gz? + String output_vcf_idx = basename(output_filename) + ".tbi" # or will this be .idx if from .vcf.gz? or ".tbi" if a .vcf command <<< set -e gatk --java-options "-Xmx2048m" \ @@ -91,6 +100,9 @@ task MergeVCFs { Array[File] input_vcf_indices String output_merged_file_name } + # TODO Ideally we wouldn't merge the vcfs at all, but keep them separated by position + # and then annotate them separately and then load each of the annotation.jsons into BQ (may involve multiple temp tables that each get mapped to the final vat) + String output_vcf = basename(output_merged_file_name) + ".vcf.gz" String output_vcf_idx = basename(output_vcf) + ".tbi" command <<< @@ -115,9 +127,9 @@ task MergeVCFs { } } -task AnnotateVCF { +task AnnotateShardedVCF { input { - File input_vcf + Array[File] input_vcfs String output_annotated_file_name File nirvana_data_tar } @@ -132,7 +144,6 @@ task AnnotateVCF { command <<< set -e - # NOTE: Validate a lil so that we don't waste time copying down the data sources if there's an error. # ======================================= # Handle our data sources: @@ -142,17 +153,24 @@ task AnnotateVCF { tar zxvf ~{nirvana_data_tar} -C datasources_dir --strip-components 2 DATA_SOURCES_FOLDER="$PWD/datasources_dir" - dotnet ~{nirvana_location} \ + # do a bash loop here to single thread annotate each of the files in the array + + for input_vcf in input_vcfs + do + dotnet ~{nirvana_location} \ -c $DATA_SOURCES_FOLDER~{path} \ --sd $DATA_SOURCES_FOLDER~{path_supplementary_annotations} \ -r $DATA_SOURCES_FOLDER~{path_reference} \ - -i ~{input_vcf} \ - -o ~{output_annotated_file_name} + -i ~{input_vcfs} \ + -o ~{output_annotated_file_name+"input_vcf letter or Ii or somethinig?"} + done + + >>> # ------------------------------------------------ # Runtime settings: runtime { - docker: "annotation/nirvana:3.14" + docker: "annotation/nirvana:3.14" # this download is too slow---can we beef this up? memory: "3 GB" cpu: "1" disks: "local-disk 100 HDD" @@ -165,27 +183,44 @@ task AnnotateVCF { } } -task PrepAnnotationJson { +task AnnotateVCF { # can we add the tar to the docker container? input { - File annotation_json - File annotation_json_jsi + File input_vcf + String output_annotated_file_name + File nirvana_data_tar } + String annotation_json_name = basename(output_annotated_file_name) + ".json.gz" + String annotation_json_name_jsi = annotation_json_name + ".jsi" - String unzipped_json = "unzipped.json" - String newline_delimited_json = "load_into_bq.json" + String nirvana_location = "/opt/nirvana/Nirvana.dll" + String path = "/Cache/GRCh38/Both" + String path_supplementary_annotations = "/SupplementaryAnnotation/GRCh38" + String path_reference = "/References/Homo_sapiens.GRCh38.Nirvana.dat" command <<< set -e - # prepare the json file for loading into BQ by making it a new line delimited json - gunzip -c ~{annotation_json} >> ~{unzipped_json} - jq -rc '.positions | .[]' ~{unzipped_json} >> ~{newline_delimited_json} + # NOTE: Validate a lil so that we don't waste time copying down the data sources if there's an error. + # ======================================= + # Handle our data sources: + # Extract the tar.gz: + echo "Extracting annotation data sources tar/gzip file..." + mkdir datasources_dir + tar zxvf ~{nirvana_data_tar} -C datasources_dir --strip-components 2 + DATA_SOURCES_FOLDER="$PWD/datasources_dir" + + dotnet ~{nirvana_location} \ + -c $DATA_SOURCES_FOLDER~{path} \ + --sd $DATA_SOURCES_FOLDER~{path_supplementary_annotations} \ + -r $DATA_SOURCES_FOLDER~{path_reference} \ + -i ~{input_vcf} \ + -o ~{output_annotated_file_name} >>> # ------------------------------------------------ # Runtime settings: runtime { - docker: "stedolan/jq:latest" + docker: "annotation/nirvana:3.14" # this download is too slow---can we beef this up? memory: "3 GB" cpu: "1" disks: "local-disk 100 HDD" @@ -193,40 +228,54 @@ task PrepAnnotationJson { # ------------------------------------------------ # Outputs: output { - File annotations_edited_file = newline_delimited_json + File annotation_json = "~{annotation_json_name}" + File annotation_json_jsi = "~{annotation_json_name_jsi}" } } task BigQueryLoadJson { input { File annotation_json - String nirvana_schema + File nirvana_schema String project_id String dataset_name } + # I am going to want to have two pre-vat tables. A variant table and a genes table + + String temp_table = "pre-vat" + String vat_table = "vatter" + command <<< set -e # load the annotation json in as a temp interim BQ vat table - TEMP_TABLE="~{dataset_name}.pre-vat" - bq --location=US load --project_id=~{project_id} --source_format=NEWLINE_DELIMITED_JSON --autodetect $TEMP_TABLE ~{annotation_json} + # TODO make sure when you load---if you split in some way, that you dont drop "header lines" from secondary shards that have no headers + + echo "Creating the pre-vat table ~{dataset_name}.~{temp_table}" + bq --location=US load --replace=true --project_id=~{project_id} --source_format=NEWLINE_DELIMITED_JSON --autodetect ~{dataset_name}.~{temp_table} ~{annotation_json} + # bq --location=US load --replace=true --project_id="spec-ops-aou" --source_format=NEWLINE_DELIMITED_JSON --autodetect "anvil_100_for_testing.temp" /Users/aurora/Desktop/repositories/gatk/hello_did_I_annotate.json # create the final vat table with the correct fields - # TODO this is a hacky set of fields---would ideally use the vat_schema.json PARTITION_FIELD="position" CLUSTERING_FIELD="vid" PARTITION_STRING="" #--range_partitioning=$PARTITION_FIELD,0,4000,4000" CLUSTERING_STRING="" #--clustering_fields=$CLUSTERING_FIELD" - TABLE="~{dataset_name}.vatter" - SCHEMA="~{nirvana_schema}" - PROJECT="~{project_id}" - echo "Creating a vat table..." - bq --location=US mk ${PARTITION_STRING} ${CLUSTERING_STRING} --project_id=~{project_id} $TABLE $SCHEMA > status_bq_submission + + set +e + bq show --project_id ~{project_id} ~{dataset_name}.~{vat_table} > /dev/null + BQ_SHOW_RC=$? + set -e + if [ $BQ_SHOW_RC -ne 0 ]; then + echo "Creating the vat table ~{dataset_name}.~{vat_table}" + bq --location=US mk --project_id=~{project_id} ~{dataset_name}.~{vat_table} ~{nirvana_schema} + fi + echo "And putting data into it" # now run some giant query in BQ to get this all in the right table - bq query --destination_table="anvil_100_for_testing.vatter" --project_id="spec-ops-aou" 'SELECT + bq query --nouse_legacy_sql --destination_table=~{dataset_name}.~{vat_table} --project_id=~{project_id} \ + 'SELECT v.position, v.vid, v.chromosome AS contig, @@ -245,31 +294,31 @@ task BigQueryLoadJson { t.introns AS intron_number, t.hgvsc AS splice_distance, t.geneId AS entrez_gene_id, - CASE WHEN ( t.transcript is not null and t.isCanonical is not True) THEN "false" WHEN ( t.transcript is not null and t.isCanonical is True) THEN "true" END AS is_canonical_transcript, - null AS gvs_all_ac, - null AS gvs_all_an, - null AS gvs_all_af, - v.revel.score AS revel, + CASE WHEN ( t.transcript is not null and t.isCanonical is not True) THEN "false" WHEN ( t.transcript is not null and t.isCanonical is True) THEN "true" END AS is_canonical_transcript, + null AS gvs_all_ac, + null AS gvs_all_an, + null AS gvs_all_af, + v.revel.score AS revel, # we just grab the first value in spliceAI (need to validate that there will only ever be one) - CASE WHEN (select array_length(v.spliceAI)) > 0 + CASE WHEN (array_length(v.spliceAI)) > 0 THEN v.spliceAI[offset(0)].acceptorGainScore END AS splice_ai_acceptor_gain_score, - CASE WHEN (select array_length(v.spliceAI)) > 0 + CASE WHEN (array_length(v.spliceAI)) > 0 THEN v.spliceAI[offset(0)].acceptorGainDistance END AS splice_ai_acceptor_gain_distance, - CASE WHEN (select array_length(v.spliceAI)) > 0 + CASE WHEN (array_length(v.spliceAI)) > 0 THEN v.spliceAI[offset(0)].acceptorLossScore END AS splice_ai_acceptor_loss_score, - CASE WHEN (select array_length(v.spliceAI)) > 0 + CASE WHEN (array_length(v.spliceAI)) > 0 THEN v.spliceAI[offset(0)].acceptorLossDistance END AS splice_ai_acceptor_loss_distance, - CASE WHEN (select array_length(v.spliceAI)) > 0 + CASE WHEN (array_length(v.spliceAI)) > 0 THEN v.spliceAI[offset(0)].donorGainScore END AS splice_ai_donor_gain_score, - CASE WHEN (select array_length(v.spliceAI)) > 0 + CASE WHEN (array_length(v.spliceAI)) > 0 THEN v.spliceAI[offset(0)].donorGainDistance END AS splice_ai_donor_gain_distance, - CASE WHEN (select array_length(v.spliceAI)) > 0 + CASE WHEN (array_length(v.spliceAI)) > 0 THEN v.spliceAI[offset(0)].donorLossScore END AS splice_ai_donor_loss_score, - CASE WHEN (select array_length(v.spliceAI)) > 0 + CASE WHEN (array_length(v.spliceAI)) > 0 THEN v.spliceAI[offset(0)].donorLossDistance END AS splice_ai_donor_loss_distance, (SELECT ARRAY_TO_STRING(significance, ",") FROM v.clinvar WHERE id LIKE "RCV%") AS clinvar_classification, (SELECT lastUpdatedDate FROM v.clinvar WHERE id LIKE "RCV%") AS clinvar_last_updated, - (SELECT ARRAY_TO_STRING(phenotypes, ",") FROM v.clinvar WHERE id LIKE "RCV%") AS clinvar_phenotype, + (SELECT phenotypes FROM v.clinvar WHERE id LIKE "RCV%") AS clinvar_phenotype, v.gnomad.allAf AS gnomad_all_af, v.gnomad.allAc AS gnomad_all_ac, v.gnomad.allAn AS gnomad_all_an, @@ -280,11 +329,13 @@ task BigQueryLoadJson { null AS gene_omim_id, null AS omim_phenotypes_id, null AS omim_phenotypes_name, - from (SELECT position, variantline.* FROM `spec-ops-aou.anvil_100_for_testing.pre-vat`, UNNEST(variants) as variantline) as v left join - (SELECT position, variantline.vid, transcriptline.* FROM `spec-ops-aou.anvil_100_for_testing.pre-vat`, UNNEST(variants) as variantline, UNNEST(variantline.transcripts) as transcriptline) as t on v.vid = t.vid' + from (SELECT position, variantline.* FROM `~{dataset_name}.~{temp_table}`, UNNEST(variants) as variantline) as v + left join (SELECT position, variantline.vid, transcriptline.* FROM `~{dataset_name}.~{temp_table}`, UNNEST(variants) as variantline, UNNEST(variantline.transcripts) as transcriptline) as t on v.vid = t.vid' + + # cat status_bq_submission | tail -n 1 > status_bq_submission_last_line # bq_job_id=$(sed 's/.*://' status_bq_submission_last_line) - #echo $bq_job_id + #echo $bq_job_id >>> # ------------------------------------------------ From b73b42a25710f4d357711de72b8eaf3762da58fb Mon Sep 17 00:00:00 2001 From: rori <6863459+RoriCremer@users.noreply.github.com> Date: Wed, 23 Jun 2021 19:14:26 -0400 Subject: [PATCH 25/73] this needs to be json-ified --- .../create_variant_annotation_table.py | 246 ++++++++++++------ 1 file changed, 168 insertions(+), 78 deletions(-) diff --git a/scripts/variantstore/wdl/extract/create_variant_annotation_table.py b/scripts/variantstore/wdl/extract/create_variant_annotation_table.py index 72d3f15fbb1..8229e84763a 100644 --- a/scripts/variantstore/wdl/extract/create_variant_annotation_table.py +++ b/scripts/variantstore/wdl/extract/create_variant_annotation_table.py @@ -19,6 +19,8 @@ VAT_TABLE_PREFIX = "vat_" SAMPLES_PER_PARTITION = 4000 +## TODO in the future I want to map the original json key to a function! + vat_nirvana_positions_dictionary = { "position": "position", # required TODO pull this out! check how nirvana handles "when the vcf position is not just the preceeding base for the variant" } @@ -79,16 +81,17 @@ "gnomad_all_af": "allAf", # nullable "gnomad_all_ac": "allAc", # nullable "gnomad_all_an": "allAn", # nullable - "gnomad_max_af": "afrAf", # nullable - "gnomad_max_ac": "afrAc", # nullable - "gnomad_max_an": "afrAn", # nullable + "gnomad_max_af": "afrAf", # nullable THIS NEEDS MORE THAN JUST A MAPPING + "gnomad_max_ac": "afrAc", # nullable THIS NEEDS MORE THAN JUST A MAPPING + "gnomad_max_an": "afrAn", # nullable THIS NEEDS MORE THAN JUST A MAPPING "gnomad_max_subpop": "x" #TODO need to choose the correct mapping. Lee says maybe drop for now } vat_nirvana_omim_dictionary = { # TODO or should this be vat_nirvana_genes_dictionary ? - "gene_omim_id": "mimNumber", # nullable - "omim_phenotypes_id": "phenotype", # nullable <-- lets talk arrays! - "omim_phenotypes_name": "x" #TODO where is the omim stuff?????? <-- lets talk arrays! + #"hgnc_gene_id": "hgncid", # nullable genes.hgncid NOT HERE?!??!? + # "gene_omim_id": "mimNumber", # nullable genes.omim.mimNumber HARD CODED FOR NOW + "omim_phenotypes_id": "mimNumber", # nullable <-- lets talk arrays! genes.omim.phenotypes.mimNumber + "omim_phenotypes_name": "phenotype" #TODO where is the omim stuff?????? <-- lets talk arrays! genes.omim.phenotypes.phenotype } def make_fieldnames(): @@ -120,7 +123,7 @@ def make_annotated_row(row_position, variant_line, transcript_line): # would it for vat_transcripts_fieldname in transcripts_fieldnames: # like "transcript" nirvana_transcripts_fieldname = vat_nirvana_transcripts_dictionary.get(vat_transcripts_fieldname) transcript_fieldvalue = transcript_line.get(nirvana_transcripts_fieldname) - if nirvana_transcripts_fieldname = "isCanonical" & transcript_fieldvalue != True: # oooof this is ugly + if nirvana_transcripts_fieldname == "isCanonical" and transcript_fieldvalue != True: # oooof this is ugly transcript_fieldvalue = False row[vat_transcripts_fieldname] = transcript_fieldvalue @@ -143,25 +146,52 @@ def make_annotated_row(row_position, variant_line, transcript_line): # would it row[vat_splice_ai_fieldname] = splice_ai_fieldvalue if variant_line.get("clinvar") != None: - clinvar_line = variant_line["clinvar"][0] # TODO I am making the huge assumption that we are only grabbing 1 - for vat_clinvar_fieldname in clinvar_fieldnames: # like "clinvar_classification" - nirvana_clinvar_fieldname = vat_nirvana_clinvar_dictionary.get(vat_clinvar_fieldname) - clinvar_fieldvalue = clinvar_line.get(nirvana_clinvar_fieldname) - row[vat_clinvar_fieldname] = clinvar_fieldvalue - - if variant_line.get("genes") != None: - omim_line = variant_line["genes"][0] # TODO I am making the huge assumption that we are only grabbing 1 - for vat_omim_fieldname in omim_fieldnames: # like "clinvar_classification" - nirvana_omim_fieldname = vat_nirvana_omim_dictionary.get(vat_omim_fieldname) - omim_fieldvalue = omim_line.get(nirvana_omim_fieldname) - row[vat_omim_fieldname] = omim_fieldvalue + clinvar_lines = variant_line["clinvar"] # TODO I am making the huge assumption that this is correctly pulling the RCV one + for clinvar_correct_line in clinvar_lines: + # get the clinvar line with the id that starts with RCV + if clinvar_correct_line.get("id")[:2] == "RCV": + for vat_clinvar_fieldname in clinvar_fieldnames: # like "clinvar_classification" + nirvana_clinvar_fieldname = vat_nirvana_clinvar_dictionary.get(vat_clinvar_fieldname) + clinvar_fieldvalue = clinvar_correct_line.get(nirvana_clinvar_fieldname) + row[vat_clinvar_fieldname] = clinvar_fieldvalue if variant_line.get("revel") != None: row["revel"] = variant_line.get("revel").get("score") return row -def make_annotation_table(annotated_json, output_csv): +def make_annotation_tables(annotated_json): + variant_transcript_table_output_csv = "aou_alpha1_shard_annotations_vat.csv" # TODO get this from the annotated_json name + genes_output_csv = "aou_alpha1_shard_annotations_vat_genes.csv" # TODO get this from the annotated_json name + # make_variant_transcript_table(annotated_json, variant_transcript_table_output_csv) + make_genes_table(annotated_json, genes_output_csv) + +def make_genes_table(annotated_json, output_csv): # why is this taking so long? I think we will want the reading to be done as a single script to make both tables + with open(output_csv, 'w', newline='') as csvfile: + omim_fieldnames = list(vat_nirvana_omim_dictionary.keys()) + fieldnames = omim_fieldnames + fieldnames.extend(["gene_symbol","gene_omim_id"]) + writer = csv.DictWriter(csvfile, fieldnames=fieldnames) + writer.writeheader() + json_data = open(annotated_json) + data = json.load(json_data) + gene_lines = data["genes"] # we want to write this out elsewhere? + for gene_line in gene_lines: + if gene_line.get("omim") != None: + row = {} + row["gene_symbol"] = gene_line.get("name") # TODO throw an error if it's None? We dont care if there's no omim tho, right? right! cuz nothin would be there to add in the join + omim_line = gene_line["omim"][0] # TODO I am making the huge assumption that we are only grabbing 1 + row["gene_omim_id"] = omim_line.get("mimNumber") + + if omim_line.get("phenotypes") != None: + phenotypes_line = omim_line["phenotypes"][0] # TODO I am making the huge assumption that we are only grabbing 1 + for vat_omim_fieldname in omim_fieldnames: # like "mimNumber", "phenotype" + nirvana_omim_fieldname = vat_nirvana_omim_dictionary.get(vat_omim_fieldname) + omim_fieldvalue = phenotypes_line.get(nirvana_omim_fieldname) + row[vat_omim_fieldname] = omim_fieldvalue + writer.writerow(row) + +def make_variant_transcript_table(annotated_json, output_csv): with open(output_csv, 'w', newline='') as csvfile: positions_fieldnames, variants_fieldnames, transcripts_fieldnames, gvs_alleles_fieldnames, revel_fieldnames, splice_ai_fieldnames, clinvar_fieldnames, gnomad_fieldnames, omim_fieldnames = make_fieldnames() fieldnames = positions_fieldnames @@ -172,7 +202,7 @@ def make_annotation_table(annotated_json, output_csv): fieldnames.extend(splice_ai_fieldnames) fieldnames.extend(clinvar_fieldnames) fieldnames.extend(gnomad_fieldnames) - fieldnames.extend(omim_fieldnames) + # fieldnames.extend(omim_fieldnames) writer = csv.DictWriter(csvfile, fieldnames=fieldnames) writer.writeheader() @@ -188,70 +218,128 @@ def make_annotation_table(annotated_json, output_csv): for variant_line in variant_lines: if variant_line.get("transcripts") == None: # then we make a special row - print("can I handle this?") row = make_annotated_row(row_position, variant_line, None) - print("could I handle this?") - print(row) writer.writerow(row) else: transcript_lines = variant_line.get("transcripts") for transcript_line in transcript_lines: row = make_annotated_row(row_position, variant_line, transcript_line) - print(row) writer.writerow(row) -""" row = {} - row["position"] = annotated_json_line.get("position") # this is a required field -- do we want validation? (what about validation for all the variants_fieldnames?) - - for vat_variants_fieldname in variants_fieldnames: # like "contig" - nirvana_variants_fieldname = vat_nirvana_variants_dictionary.get(vat_variants_fieldname) - variant_fieldvalue = variant_line.get(nirvana_variants_fieldname) - row[vat_variants_fieldname] = variant_fieldvalue - - for vat_transcripts_fieldname in transcripts_fieldnames: # like "transcript" - nirvana_transcripts_fieldname = vat_nirvana_transcripts_dictionary.get(vat_transcripts_fieldname) - transcript_fieldvalue = transcript_line.get(nirvana_transcripts_fieldname) - row[vat_transcripts_fieldname] = transcript_fieldvalue - - for vat_gvs_alleles_fieldname in gvs_alleles_fieldnames: # like "gvs_all_ac" - nirvana_gvs_alleles_fieldname = vat_nirvana_gvs_alleles_dictionary.get(vat_gvs_alleles_fieldname) - gvs_alleles_fieldvalue = variant_line.get(nirvana_gvs_alleles_fieldname) - row[vat_gvs_alleles_fieldname] = gvs_alleles_fieldvalue - - if variant_line.get("gnomad") != None: - for vat_gnomad_fieldname in gnomad_fieldnames: # like "gnomad_all_af" - nirvana_gnomad_fieldname = vat_nirvana_gnomad_dictionary.get(vat_gnomad_fieldname) - gnomad_fieldvalue = variant_line.get("gnomad").get(nirvana_gnomad_fieldname) # not a list like the others - row[vat_gnomad_fieldname] = gnomad_fieldvalue - - if variant_line.get("spliceAI") != None: - splice_ai_line = variant_line["spliceAI"][0] # TODO I am making the huge assumption that we are only grabbing 1 - for vat_splice_ai_fieldname in splice_ai_fieldnames: # like "splice_ai_acceptor_gain_score" - nirvana_splice_ai_fieldname = vat_nirvana_splice_ai_dictionary.get(vat_splice_ai_fieldname) - splice_ai_fieldvalue = splice_ai_line.get(nirvana_splice_ai_fieldname) - row[vat_splice_ai_fieldname] = splice_ai_fieldvalue - - if variant_line.get("clinvar") != None: - clinvar_line = variant_line["clinvar"][0] # TODO I am making the huge assumption that we are only grabbing 1 - for vat_clinvar_fieldname in clinvar_fieldnames: # like "clinvar_classification" - nirvana_clinvar_fieldname = vat_nirvana_clinvar_dictionary.get(vat_clinvar_fieldname) - clinvar_fieldvalue = clinvar_line.get(nirvana_clinvar_fieldname) - row[vat_clinvar_fieldname] = clinvar_fieldvalue - - if variant_line.get("genes") != None: - omim_line = variant_line["genes"][0] # TODO I am making the huge assumption that we are only grabbing 1 - for vat_omim_fieldname in omim_fieldnames: # like "clinvar_classification" - nirvana_omim_fieldname = vat_nirvana_omim_dictionary.get(vat_omim_fieldname) - omim_fieldvalue = omim_line.get(nirvana_omim_fieldname) - row[vat_omim_fieldname] = omim_fieldvalue - - if variant_line.get("revel") != None: - row["revel"] = variant_line.get("revel").get("score") - - - print(row) - writer.writerow(row)""" +def make_annotation_json(annotated_json, output_json): + output_file=open(output_json, 'w') + json_data = open(annotated_json, 'r') + data = json.load(json_data) + annotated_json_lines = data['positions'] + for annotated_json_line in annotated_json_lines: + position=annotated_json_line.get('position') + variants=annotated_json_line.get('variants') + for variant in variants: + make_variant_line={} # remember that we want one for each variant-transcript and variant-null for variants without transcripts + make_variant_line['position']=position + for value in vat_nirvana_variants_dictionary.values(): + make_variant_line[value]=variant.get(value) + if variant.get("revel") != None: # TODO check with Lee to see if this spacing is safe -- if there are no transcripts will there always never be a revel, spliceAT etc? + make_variant_line["revel"] = variant.get("revel").get("score") + if variant.get("spliceAI") != None: + spliceAI_first_item = variant.get("spliceAI")[0] + make_variant_line["spliceAI"]={} + for value in vat_nirvana_splice_ai_dictionary.values(): + make_variant_line["spliceAI"][value]=spliceAI_first_item.get(value) # TODO I am making the huge assumption that we are only grabbing the first + if variant.get("clinvar") != None: + clinvar_items = variant.get("clinvar") + make_variant_line["clinvar"]={} + for clinvar_item in clinvar_items: + if clinvar_item.get("id")[:3] == "RCV": # would it be better to save this processing for in BQ? + for value in vat_nirvana_clinvar_dictionary.values(): + make_variant_line["clinvar"][value]=clinvar_item.get(value) + if variant.get("gnomad") != None: + make_variant_line["gnomad"]={} + for value in vat_nirvana_gnomad_dictionary.values(): + make_variant_line["gnomad"][value]=variant.get("gnomad").get(value) + if variant.get("transcripts") == None: + back_json=json.dumps(make_variant_line) + output_file.write(back_json) + output_file.write("\n") + else: + transcript_lines = variant.get("transcripts") + for transcript_line in transcript_lines: + make_transcript_line=make_variant_line # remember that we want one for each variant-transcript and variant-null for variants without transcripts + for value in vat_nirvana_transcripts_dictionary.values(): + make_transcript_line[value]=transcript_line.get(value) + back_json=json.dumps(make_transcript_line) + output_file.write(back_json) + output_file.write("\n") + output_file.close() + +def make_annotation_json_better(annotated_json, output_json): + output_file=open(output_json, 'w') + json_data = open(annotated_json, 'r') + data = json.load(json_data) + annotated_position_json_lines = data['positions'] + annotated_genes_json_lines = data['genes'] + for annotated_json_line in annotated_position_json_lines: + position=annotated_json_line.get('position') + variants=annotated_json_line.get('variants') + + row_position = annotated_json_line.get("position") # this is a required field -- do we want validation? + # want to write a csv row for each variant - transcript + # so let's start with each variant + variant_lines = annotated_json_line.get("variants") # this is a required field -- do we want validation? + for variant_line in variant_lines: + if variant_line.get("transcripts") == None: + # then we make a special row + row = make_annotated_row(row_position, variant_line, None) + writer.writerow(row) + else: + transcript_lines = variant_line.get("transcripts") + for transcript_line in transcript_lines: + row = make_annotated_row(row_position, variant_line, transcript_line) + writer.writerow(row) + + + for annotated_json_line in annotated_position_json_lines: + position=annotated_json_line.get('position') + variants=annotated_json_line.get('variants') + for variant in variants: + make_variant_line={} # remember that we want one for each variant-transcript and variant-null for variants without transcripts + make_variant_line['position']=position + for variant_entry in vat_nirvana_variants_dictionary: + #this needs help + make_variant_line[variant_entry.key()]=variant.get(variant_entry.value()) + if variant.get("revel") != None: # TODO check with Lee to see if this spacing is safe -- if there are no transcripts will there always never be a revel, spliceAT etc? + make_variant_line["revel"] = variant.get("revel").get("score") + if variant.get("spliceAI") != None: + spliceAI_first_item = variant.get("spliceAI")[0] + make_variant_line["spliceAI"]={} + for value in vat_nirvana_splice_ai_dictionary.values(): + make_variant_line["spliceAI"][value]=spliceAI_first_item.get(value) # TODO I am making the huge assumption that we are only grabbing the first + if variant.get("clinvar") != None: + clinvar_items = variant.get("clinvar") + make_variant_line["clinvar"]={} + for clinvar_item in clinvar_items: + if clinvar_item.get("id")[:3] == "RCV": # would it be better to save this processing for in BQ? + for value in vat_nirvana_clinvar_dictionary.values(): + make_variant_line["clinvar"][value]=clinvar_item.get(value) + if variant.get("gnomad") != None: + make_variant_line["gnomad"]={} + for value in vat_nirvana_gnomad_dictionary.values(): + make_variant_line["gnomad"][value]=variant.get("gnomad").get(value) + if variant.get("transcripts") == None: + back_json=json.dumps(make_variant_line) + output_file.write(back_json) + output_file.write("\n") + else: + transcript_lines = variant.get("transcripts") + for transcript_line in transcript_lines: + make_transcript_line=make_variant_line # remember that we want one for each variant-transcript and variant-null for variants without transcripts + for value in vat_nirvana_transcripts_dictionary.values(): + make_transcript_line[value]=transcript_line.get(value) + back_json=json.dumps(make_transcript_line) + output_file.write(back_json) + output_file.write("\n") + output_file.close() """ if __name__ == '__main__': parser = argparse.ArgumentParser(allow_abbrev=False, description='Extract a cohort from BigQuery Variant Store ') @@ -261,6 +349,8 @@ def make_annotation_table(annotated_json, output_csv): # Execute the parse_args() method args = parser.parse_args() - make_annotation_table(annotated_json) """ + make_annotation_tables(annotated_json) """ -make_annotation_table("hello_did_I_annotate.json", "vat_annotations.csv") +make_annotation_tables("ralpha1.json") +#make_annotation_json_better("ralpha1.json", "aou_alpha1_shard_annotations_bq_load.json") +#make_annotation_json("ralpha1.json", "aou_alpha1_shard_annotations_bq_load.json") From ad7a78dfb6e6412ae65338d5971711a379ff9383 Mon Sep 17 00:00:00 2001 From: rori <6863459+RoriCremer@users.noreply.github.com> Date: Thu, 24 Jun 2021 11:23:19 -0400 Subject: [PATCH 26/73] wdl idea --- scripts/variantstore/wdl/GvsSitesOnlyVCF.wdl | 2 ++ 1 file changed, 2 insertions(+) diff --git a/scripts/variantstore/wdl/GvsSitesOnlyVCF.wdl b/scripts/variantstore/wdl/GvsSitesOnlyVCF.wdl index eb30502f30d..0e189268393 100644 --- a/scripts/variantstore/wdl/GvsSitesOnlyVCF.wdl +++ b/scripts/variantstore/wdl/GvsSitesOnlyVCF.wdl @@ -242,6 +242,8 @@ task BigQueryLoadJson { } # I am going to want to have two pre-vat tables. A variant table and a genes table + # See if + we can grab the annotations json directly from the gcp bucket (so pull it in as a string so it wont) String temp_table = "pre-vat" String vat_table = "vatter" From 6aa56f06ede5943260eeb5880cb22e3d328b8df1 Mon Sep 17 00:00:00 2001 From: rori <6863459+RoriCremer@users.noreply.github.com> Date: Thu, 24 Jun 2021 11:23:59 -0400 Subject: [PATCH 27/73] update vat schema for json upload --- scripts/variantstore/wdl/schemas/vat_schema.json | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/scripts/variantstore/wdl/schemas/vat_schema.json b/scripts/variantstore/wdl/schemas/vat_schema.json index 8730d52dc2a..a2c93726ed8 100644 --- a/scripts/variantstore/wdl/schemas/vat_schema.json +++ b/scripts/variantstore/wdl/schemas/vat_schema.json @@ -42,10 +42,10 @@ "mode": "Required" }, { - "description": "rsID", + "description": "rsID TODO check with Lee about why this json thinks its Repeated not nullable", "name": "dbsnp_rsid", "type": "String", - "mode": "Nullable" + "mode": "Repeated" }, { "description": "Transcript ID. Null indicates that this variant does not overlap any transcripts", @@ -72,10 +72,10 @@ "mode": "Nullable" }, { - "description": "Amino acid change type", + "description": "Amino acid change type TODO check with Lee about why this json thinks its Repeated not nullable", "name": "consequence", "type": "String", - "mode": "Nullable" + "mode": "Repeated" }, { "description": "HGVS c. nomenclature; DNA change", @@ -110,7 +110,7 @@ { "description": "Primary Transcript ID", "name": "is_canonical_transcript", - "type": "String", + "type": "Boolean", "mode": "Nullable" }, { From 15eabc679c2c0073d351092962bbbdf495b53297 Mon Sep 17 00:00:00 2001 From: rori <6863459+RoriCremer@users.noreply.github.com> Date: Thu, 24 Jun 2021 11:28:01 -0400 Subject: [PATCH 28/73] genes json is right, positions json needs help --- .../create_variant_annotation_table.py | 139 +++++++++++------- 1 file changed, 83 insertions(+), 56 deletions(-) diff --git a/scripts/variantstore/wdl/extract/create_variant_annotation_table.py b/scripts/variantstore/wdl/extract/create_variant_annotation_table.py index 8229e84763a..43bc18fd968 100644 --- a/scripts/variantstore/wdl/extract/create_variant_annotation_table.py +++ b/scripts/variantstore/wdl/extract/create_variant_annotation_table.py @@ -107,7 +107,56 @@ def make_fieldnames(): return positions_fieldnames, variants_fieldnames, transcripts_fieldnames, gvs_alleles_fieldnames, revel_fieldnames, splice_ai_fieldnames, clinvar_fieldnames, gnomad_fieldnames, omim_fieldnames +def make_annotated_json_row(row_position, variant_line, transcript_line): # would it be better to not pass the transcript_line since its dupe data? + positions_fieldnames, variants_fieldnames, transcripts_fieldnames, gvs_alleles_fieldnames, revel_fieldnames, splice_ai_fieldnames, clinvar_fieldnames, gnomad_fieldnames, omim_fieldnames = make_fieldnames() + row = {} + row["position"] = row_position # this is a required field -- do we want validation? (what about validation for all the variants_fieldnames?) + + for vat_variants_fieldname in variants_fieldnames: # like "contig" + nirvana_variants_fieldname = vat_nirvana_variants_dictionary.get(vat_variants_fieldname) + variant_fieldvalue = variant_line.get(nirvana_variants_fieldname) + row[vat_variants_fieldname] = variant_fieldvalue + + if transcript_line != None: + for vat_transcripts_fieldname in transcripts_fieldnames: # like "transcript" + nirvana_transcripts_fieldname = vat_nirvana_transcripts_dictionary.get(vat_transcripts_fieldname) + transcript_fieldvalue = transcript_line.get(nirvana_transcripts_fieldname) + if nirvana_transcripts_fieldname == "isCanonical" and transcript_fieldvalue != True: # oooof this is ugly + transcript_fieldvalue = False + row[vat_transcripts_fieldname] = transcript_fieldvalue + + for vat_gvs_alleles_fieldname in gvs_alleles_fieldnames: # like "gvs_all_ac" + nirvana_gvs_alleles_fieldname = vat_nirvana_gvs_alleles_dictionary.get(vat_gvs_alleles_fieldname) + gvs_alleles_fieldvalue = variant_line.get(nirvana_gvs_alleles_fieldname) + row[vat_gvs_alleles_fieldname] = gvs_alleles_fieldvalue + + if variant_line.get("gnomad") != None: + for vat_gnomad_fieldname in gnomad_fieldnames: # like "gnomad_all_af" + nirvana_gnomad_fieldname = vat_nirvana_gnomad_dictionary.get(vat_gnomad_fieldname) + gnomad_fieldvalue = variant_line.get("gnomad").get(nirvana_gnomad_fieldname) # not a list like the others + row[vat_gnomad_fieldname] = gnomad_fieldvalue + + if variant_line.get("spliceAI") != None: + splice_ai_line = variant_line["spliceAI"][0] # TODO I am making the huge assumption that we are only grabbing 1 + for vat_splice_ai_fieldname in splice_ai_fieldnames: # like "splice_ai_acceptor_gain_score" + nirvana_splice_ai_fieldname = vat_nirvana_splice_ai_dictionary.get(vat_splice_ai_fieldname) + splice_ai_fieldvalue = splice_ai_line.get(nirvana_splice_ai_fieldname) + row[vat_splice_ai_fieldname] = splice_ai_fieldvalue + + if variant_line.get("clinvar") != None: + clinvar_lines = variant_line["clinvar"] # TODO I am making the huge assumption that this is correctly pulling the RCV one + for clinvar_correct_line in clinvar_lines: + # get the clinvar line with the id that starts with RCV + if clinvar_correct_line.get("id")[:2] == "RCV": + for vat_clinvar_fieldname in clinvar_fieldnames: # like "clinvar_classification" + nirvana_clinvar_fieldname = vat_nirvana_clinvar_dictionary.get(vat_clinvar_fieldname) + clinvar_fieldvalue = clinvar_correct_line.get(nirvana_clinvar_fieldname) + row[vat_clinvar_fieldname] = clinvar_fieldvalue + if variant_line.get("revel") != None: + row["revel"] = variant_line.get("revel").get("score") + + return row def make_annotated_row(row_position, variant_line, transcript_line): # would it be better to not pass the transcript_line since its dupe data? positions_fieldnames, variants_fieldnames, transcripts_fieldnames, gvs_alleles_fieldnames, revel_fieldnames, splice_ai_fieldnames, clinvar_fieldnames, gnomad_fieldnames, omim_fieldnames = make_fieldnames() @@ -273,73 +322,51 @@ def make_annotation_json(annotated_json, output_json): output_file.write("\n") output_file.close() -def make_annotation_json_better(annotated_json, output_json): +def make_annotation_json_better(annotated_json, output_json, output_genes_json): output_file=open(output_json, 'w') + output_genes_file=open(output_genes_json, 'w') json_data = open(annotated_json, 'r') data = json.load(json_data) - annotated_position_json_lines = data['positions'] - annotated_genes_json_lines = data['genes'] - for annotated_json_line in annotated_position_json_lines: - position=annotated_json_line.get('position') - variants=annotated_json_line.get('variants') - - row_position = annotated_json_line.get("position") # this is a required field -- do we want validation? - # want to write a csv row for each variant - transcript - # so let's start with each variant - variant_lines = annotated_json_line.get("variants") # this is a required field -- do we want validation? - for variant_line in variant_lines: - if variant_line.get("transcripts") == None: - # then we make a special row - row = make_annotated_row(row_position, variant_line, None) - writer.writerow(row) - else: - transcript_lines = variant_line.get("transcripts") - for transcript_line in transcript_lines: - row = make_annotated_row(row_position, variant_line, transcript_line) - writer.writerow(row) - - - for annotated_json_line in annotated_position_json_lines: - position=annotated_json_line.get('position') + annotated_position_lines = data['positions'] + annotated_gene_lines = data['genes'] + for annotated_json_line in annotated_position_lines: + position=annotated_json_line.get('position') # this is a required field -- do we want validation? variants=annotated_json_line.get('variants') + # row for each variant - transcript + # so let's start with each variant for variant in variants: - make_variant_line={} # remember that we want one for each variant-transcript and variant-null for variants without transcripts - make_variant_line['position']=position - for variant_entry in vat_nirvana_variants_dictionary: - #this needs help - make_variant_line[variant_entry.key()]=variant.get(variant_entry.value()) - if variant.get("revel") != None: # TODO check with Lee to see if this spacing is safe -- if there are no transcripts will there always never be a revel, spliceAT etc? - make_variant_line["revel"] = variant.get("revel").get("score") - if variant.get("spliceAI") != None: - spliceAI_first_item = variant.get("spliceAI")[0] - make_variant_line["spliceAI"]={} - for value in vat_nirvana_splice_ai_dictionary.values(): - make_variant_line["spliceAI"][value]=spliceAI_first_item.get(value) # TODO I am making the huge assumption that we are only grabbing the first - if variant.get("clinvar") != None: - clinvar_items = variant.get("clinvar") - make_variant_line["clinvar"]={} - for clinvar_item in clinvar_items: - if clinvar_item.get("id")[:3] == "RCV": # would it be better to save this processing for in BQ? - for value in vat_nirvana_clinvar_dictionary.values(): - make_variant_line["clinvar"][value]=clinvar_item.get(value) - if variant.get("gnomad") != None: - make_variant_line["gnomad"]={} - for value in vat_nirvana_gnomad_dictionary.values(): - make_variant_line["gnomad"][value]=variant.get("gnomad").get(value) + # remember that we want one for each variant-transcript and variant-null for variants without transcripts if variant.get("transcripts") == None: - back_json=json.dumps(make_variant_line) + # then we make a special row + row = make_annotated_json_row(position, variant, None) + back_json=json.dumps(row) output_file.write(back_json) output_file.write("\n") else: transcript_lines = variant.get("transcripts") - for transcript_line in transcript_lines: - make_transcript_line=make_variant_line # remember that we want one for each variant-transcript and variant-null for variants without transcripts - for value in vat_nirvana_transcripts_dictionary.values(): - make_transcript_line[value]=transcript_line.get(value) - back_json=json.dumps(make_transcript_line) + for transcript in transcript_lines: + row = make_annotated_json_row(position, variant, transcript) + back_json=json.dumps(row) output_file.write(back_json) output_file.write("\n") output_file.close() + omim_fieldnames = list(vat_nirvana_omim_dictionary.keys()) + for gene_line in annotated_gene_lines: + if gene_line.get("omim") != None: + row = {} + row["gene_symbol"] = gene_line.get("name") # TODO throw an error if it's None? We dont care if there's no omim tho, right? right! cuz nothin would be there to add in the join + omim_line = gene_line["omim"][0] # TODO I am making the huge assumption that we are only grabbing 1 + row["gene_omim_id"] = omim_line.get("mimNumber") + if omim_line.get("phenotypes") != None: + phenotypes_line = omim_line["phenotypes"][0] # TODO I am making the huge assumption that we are only grabbing 1 + for vat_omim_fieldname in omim_fieldnames: # like "mimNumber", "phenotype" + nirvana_omim_fieldname = vat_nirvana_omim_dictionary.get(vat_omim_fieldname) + omim_fieldvalue = phenotypes_line.get(nirvana_omim_fieldname) + row[vat_omim_fieldname] = omim_fieldvalue + back_json=json.dumps(row) + output_genes_file.write(back_json) + aou_shard_223_vatteroutput_genes_file.write("\n") + output_genes_file.close() """ if __name__ == '__main__': parser = argparse.ArgumentParser(allow_abbrev=False, description='Extract a cohort from BigQuery Variant Store ') @@ -351,6 +378,6 @@ def make_annotation_json_better(annotated_json, output_json): make_annotation_tables(annotated_json) """ -make_annotation_tables("ralpha1.json") -#make_annotation_json_better("ralpha1.json", "aou_alpha1_shard_annotations_bq_load.json") +#make_annotation_tables("ralpha1.json") +make_annotation_json_better("ralpha1.json", "aou_alpha1_shard_annotations_bq_load.json", "aou_alpha1_shard_genes_bq_load.json") #make_annotation_json("ralpha1.json", "aou_alpha1_shard_annotations_bq_load.json") From 7e69606cb4f19be4cfea3b013d306dea4e109f17 Mon Sep 17 00:00:00 2001 From: rori <6863459+RoriCremer@users.noreply.github.com> Date: Thu, 24 Jun 2021 14:42:59 -0400 Subject: [PATCH 29/73] updating the query in the WDL --- scripts/variantstore/wdl/GvsSitesOnlyVCF.wdl | 131 ++++++++++--------- 1 file changed, 72 insertions(+), 59 deletions(-) diff --git a/scripts/variantstore/wdl/GvsSitesOnlyVCF.wdl b/scripts/variantstore/wdl/GvsSitesOnlyVCF.wdl index 0e189268393..0734c3beff9 100644 --- a/scripts/variantstore/wdl/GvsSitesOnlyVCF.wdl +++ b/scripts/variantstore/wdl/GvsSitesOnlyVCF.wdl @@ -44,12 +44,12 @@ workflow GvsSitesOnlyVCF { # tested with "gs://broad-dsp-spec-ops/scratch/rcreme # nirvana_data_tar = nirvana_data_directory #} - # call PrepAnnotationJson { # prep w a python script-- we are assuming BQ docker has python? + # call PrepAnnotationJson { # TODO should this be it's own step? We need to run a python script to prep the jsons for bq # input: # annotation_json = AnnotateVCF.annotation_json, # } - # call BigQueryLoadJson { + # call BigQueryLoadJson { # If we dont use the above step to prep w a python script-- we are assuming BQ docker has python # input: # annotation_json = AnnotateVCF.annotation_json, # #annotation_json_jsi = AnnotateVCF.annotation_json_jsi @@ -241,12 +241,18 @@ task BigQueryLoadJson { String dataset_name } - # I am going to want to have two pre-vat tables. A variant table and a genes table - # See if - we can grab the annotations json directly from the gcp bucket (so pull it in as a string so it wont) + # I am going to want to have two pre-vat tables. A variant table and a genes table. They will be joined together for the vat table + # See if we can grab the annotations json directly from the gcp bucket (so pull it in as a string so it wont) - String temp_table = "pre-vat" String vat_table = "vatter" + String variant_transcript_table = "vat_vt" + String genes_table = "vat_genes" + + # instead of the annotation_json we now need two jsons which are created from the annotation_json with a python script + # TODO run that python script on the annotation_json + # we will also want specific schemas for each of these tables---right now we are over-using one. Let's get Lee's sign off on the final one + File variant_transcript_bq_load.json = annotation_json + File genes_bq_load.json = annotation_json command <<< set -e @@ -254,10 +260,24 @@ task BigQueryLoadJson { # load the annotation json in as a temp interim BQ vat table # TODO make sure when you load---if you split in some way, that you dont drop "header lines" from secondary shards that have no headers - echo "Creating the pre-vat table ~{dataset_name}.~{temp_table}" - bq --location=US load --replace=true --project_id=~{project_id} --source_format=NEWLINE_DELIMITED_JSON --autodetect ~{dataset_name}.~{temp_table} ~{annotation_json} + # since we expect to add to these tables, --replace=true is not a flag we want. Verify that this will not be loaded with a bq * + echo "Creating a pre-vat table ~{dataset_name}.~{variant_transcript_table}" + bq --location=US load --project_id=~{project_id} --source_format=NEWLINE_DELIMITED_JSON --autodetect ~{dataset_name}.~{variant_transcript_table} ~{variant_transcript_bq_load.json} # bq --location=US load --replace=true --project_id="spec-ops-aou" --source_format=NEWLINE_DELIMITED_JSON --autodetect "anvil_100_for_testing.temp" /Users/aurora/Desktop/repositories/gatk/hello_did_I_annotate.json + echo "Creating a pre-vat table ~{dataset_name}.~{genes_table}" + bq --location=US load --project_id=~{project_id} --source_format=NEWLINE_DELIMITED_JSON --autodetect ~{dataset_name}.~{genes_table} ~{genes_bq_load.json} + + set +e + bq show --project_id ~{project_id} ~{dataset_name}.~{vat_table} > /dev/null + BQ_SHOW_RC=$? + set -e + if [ $BQ_SHOW_RC -ne 0 ]; then + echo "Creating the vat table ~{dataset_name}.~{vat_table}" + bq --location=US mk --project_id=~{project_id} ~{dataset_name}.~{vat_table} ~{nirvana_schema} + fi + + # create the final vat table with the correct fields PARTITION_FIELD="position" CLUSTERING_FIELD="vid" @@ -278,62 +298,55 @@ task BigQueryLoadJson { # now run some giant query in BQ to get this all in the right table bq query --nouse_legacy_sql --destination_table=~{dataset_name}.~{vat_table} --project_id=~{project_id} \ 'SELECT - v.position, v.vid, - v.chromosome AS contig, - v.refAllele AS ref_allele, - v.altAllele AS alt_allele, - v.variantType AS variant_type, - v.hgvsg AS genomic_location, - ARRAY_TO_STRING(v.dbsnp, ",") AS dbsnp_rsid, - t.transcript, - t.hgnc AS gene_symbol, - t.source AS transcript_source, - t.hgvsp AS aa_change, - ARRAY_TO_STRING(t.consequence, ",") AS consequence, - t.hgvsc AS dna_change, - t.exons AS exon_number, - t.introns AS intron_number, - t.hgvsc AS splice_distance, - t.geneId AS entrez_gene_id, - CASE WHEN ( t.transcript is not null and t.isCanonical is not True) THEN "false" WHEN ( t.transcript is not null and t.isCanonical is True) THEN "true" END AS is_canonical_transcript, + v.transcript, + v.contig, + v.position, + v.ref_allele, + v.alt_allele, null AS gvs_all_ac, null AS gvs_all_an, null AS gvs_all_af, - v.revel.score AS revel, - # we just grab the first value in spliceAI (need to validate that there will only ever be one) - CASE WHEN (array_length(v.spliceAI)) > 0 - THEN v.spliceAI[offset(0)].acceptorGainScore END AS splice_ai_acceptor_gain_score, - CASE WHEN (array_length(v.spliceAI)) > 0 - THEN v.spliceAI[offset(0)].acceptorGainDistance END AS splice_ai_acceptor_gain_distance, - CASE WHEN (array_length(v.spliceAI)) > 0 - THEN v.spliceAI[offset(0)].acceptorLossScore END AS splice_ai_acceptor_loss_score, - CASE WHEN (array_length(v.spliceAI)) > 0 - THEN v.spliceAI[offset(0)].acceptorLossDistance END AS splice_ai_acceptor_loss_distance, - CASE WHEN (array_length(v.spliceAI)) > 0 - THEN v.spliceAI[offset(0)].donorGainScore END AS splice_ai_donor_gain_score, - CASE WHEN (array_length(v.spliceAI)) > 0 - THEN v.spliceAI[offset(0)].donorGainDistance END AS splice_ai_donor_gain_distance, - CASE WHEN (array_length(v.spliceAI)) > 0 - THEN v.spliceAI[offset(0)].donorLossScore END AS splice_ai_donor_loss_score, - CASE WHEN (array_length(v.spliceAI)) > 0 - THEN v.spliceAI[offset(0)].donorLossDistance END AS splice_ai_donor_loss_distance, - (SELECT ARRAY_TO_STRING(significance, ",") FROM v.clinvar WHERE id LIKE "RCV%") AS clinvar_classification, - (SELECT lastUpdatedDate FROM v.clinvar WHERE id LIKE "RCV%") AS clinvar_last_updated, - (SELECT phenotypes FROM v.clinvar WHERE id LIKE "RCV%") AS clinvar_phenotype, - v.gnomad.allAf AS gnomad_all_af, - v.gnomad.allAc AS gnomad_all_ac, - v.gnomad.allAn AS gnomad_all_an, - v.gnomad.afrAf AS gnomad_max_af, - v.gnomad.afrAc AS gnomad_max_ac, - v.gnomad.afrAn AS gnomad_max_an, + v.gene_symbol, + v.transcript_source, + v.aa_change, + ARRAY_TO_STRING(v.consequence, ",") AS consequence, + v.dna_change, + v.variant_type, + v.exon_number, + v.intron_number, + v.genomic_location, + #v.hgvsc AS splice_distance has not yet been designed + ARRAY_TO_STRING(v.dbsnp_rsid, ",") AS dbsnp_rsid, + v.entrez_gene_id, + #g.hgnc_gene_id is not produced by Nirvana annotations + g.gene_omim_id, + CASE WHEN ( v.transcript is not null and v.is_canonical_transcript is not True) + THEN "false" WHEN ( v.transcript is not null and v.is_canonical_transcript is True) THEN "true" END AS is_canonical_transcript, + v.gnomad_all_af, + v.gnomad_all_ac, + v.gnomad_all_an, + v.gnomad_max_af, # this still needs to be designed + v.gnomad_max_ac, # this still needs to be designed + v.gnomad_max_an, # this still needs to be designed null AS gnomad_max_subpop, # what is this mapping? - null AS gene_omim_id, - null AS omim_phenotypes_id, - null AS omim_phenotypes_name, - from (SELECT position, variantline.* FROM `~{dataset_name}.~{temp_table}`, UNNEST(variants) as variantline) as v - left join (SELECT position, variantline.vid, transcriptline.* FROM `~{dataset_name}.~{temp_table}`, UNNEST(variants) as variantline, UNNEST(variantline.transcripts) as transcriptline) as t on v.vid = t.vid' - + v.revel, + # this is the first value in spliceAI (need to validate that there will only ever be one) + v.splice_ai_acceptor_gain_score, + v.splice_ai_acceptor_gain_distance, + v.splice_ai_acceptor_loss_score, + v.splice_ai_acceptor_loss_distance, + v.splice_ai_donor_gain_score, + v.splice_ai_donor_gain_distance, + v.splice_ai_donor_loss_score, + v.splice_ai_donor_loss_distance, + g.omim_phenotypes_id, + g.omim_phenotypes_name, + v.clinvar_classification, # validate that we only grab lines WHERE id LIKE "RCV%" + v.clinvar_last_updated, + v.clinvar_phenotype, + from `~{dataset_name}.~{variant_transcript_table}` as v + left join `~{dataset_name}.~{genes_table}` as g on v.gene_symbol = g.gene_symbol' # cat status_bq_submission | tail -n 1 > status_bq_submission_last_line # bq_job_id=$(sed 's/.*://' status_bq_submission_last_line) From d31678e0a273c07d48925a6efe708108c02779ee Mon Sep 17 00:00:00 2001 From: rori <6863459+RoriCremer@users.noreply.github.com> Date: Thu, 24 Jun 2021 14:49:12 -0400 Subject: [PATCH 30/73] clean up python script --- .../create_variant_annotation_table.py | 194 +----------------- 1 file changed, 7 insertions(+), 187 deletions(-) diff --git a/scripts/variantstore/wdl/extract/create_variant_annotation_table.py b/scripts/variantstore/wdl/extract/create_variant_annotation_table.py index 43bc18fd968..e2b44d04c65 100644 --- a/scripts/variantstore/wdl/extract/create_variant_annotation_table.py +++ b/scripts/variantstore/wdl/extract/create_variant_annotation_table.py @@ -19,7 +19,7 @@ VAT_TABLE_PREFIX = "vat_" SAMPLES_PER_PARTITION = 4000 -## TODO in the future I want to map the original json key to a function! +## TODO in the future do I want to map the original json key to a function!?!?!?!? vat_nirvana_positions_dictionary = { "position": "position", # required TODO pull this out! check how nirvana handles "when the vcf position is not just the preceeding base for the variant" @@ -94,72 +94,7 @@ "omim_phenotypes_name": "phenotype" #TODO where is the omim stuff?????? <-- lets talk arrays! genes.omim.phenotypes.phenotype } -def make_fieldnames(): - positions_fieldnames = list(vat_nirvana_positions_dictionary.keys()) - variants_fieldnames = list(vat_nirvana_variants_dictionary.keys()) - transcripts_fieldnames = list(vat_nirvana_transcripts_dictionary.keys()) - gvs_alleles_fieldnames = list(vat_nirvana_gvs_alleles_dictionary.keys()) - revel_fieldnames = list(vat_nirvana_revel_dictionary) - splice_ai_fieldnames = list(vat_nirvana_splice_ai_dictionary.keys()) - clinvar_fieldnames = list(vat_nirvana_clinvar_dictionary.keys()) - gnomad_fieldnames = list(vat_nirvana_gnomad_dictionary.keys()) - omim_fieldnames = list(vat_nirvana_omim_dictionary.keys()) - - return positions_fieldnames, variants_fieldnames, transcripts_fieldnames, gvs_alleles_fieldnames, revel_fieldnames, splice_ai_fieldnames, clinvar_fieldnames, gnomad_fieldnames, omim_fieldnames - def make_annotated_json_row(row_position, variant_line, transcript_line): # would it be better to not pass the transcript_line since its dupe data? - positions_fieldnames, variants_fieldnames, transcripts_fieldnames, gvs_alleles_fieldnames, revel_fieldnames, splice_ai_fieldnames, clinvar_fieldnames, gnomad_fieldnames, omim_fieldnames = make_fieldnames() - row = {} - row["position"] = row_position # this is a required field -- do we want validation? (what about validation for all the variants_fieldnames?) - - for vat_variants_fieldname in variants_fieldnames: # like "contig" - nirvana_variants_fieldname = vat_nirvana_variants_dictionary.get(vat_variants_fieldname) - variant_fieldvalue = variant_line.get(nirvana_variants_fieldname) - row[vat_variants_fieldname] = variant_fieldvalue - - if transcript_line != None: - for vat_transcripts_fieldname in transcripts_fieldnames: # like "transcript" - nirvana_transcripts_fieldname = vat_nirvana_transcripts_dictionary.get(vat_transcripts_fieldname) - transcript_fieldvalue = transcript_line.get(nirvana_transcripts_fieldname) - if nirvana_transcripts_fieldname == "isCanonical" and transcript_fieldvalue != True: # oooof this is ugly - transcript_fieldvalue = False - row[vat_transcripts_fieldname] = transcript_fieldvalue - - for vat_gvs_alleles_fieldname in gvs_alleles_fieldnames: # like "gvs_all_ac" - nirvana_gvs_alleles_fieldname = vat_nirvana_gvs_alleles_dictionary.get(vat_gvs_alleles_fieldname) - gvs_alleles_fieldvalue = variant_line.get(nirvana_gvs_alleles_fieldname) - row[vat_gvs_alleles_fieldname] = gvs_alleles_fieldvalue - - if variant_line.get("gnomad") != None: - for vat_gnomad_fieldname in gnomad_fieldnames: # like "gnomad_all_af" - nirvana_gnomad_fieldname = vat_nirvana_gnomad_dictionary.get(vat_gnomad_fieldname) - gnomad_fieldvalue = variant_line.get("gnomad").get(nirvana_gnomad_fieldname) # not a list like the others - row[vat_gnomad_fieldname] = gnomad_fieldvalue - - if variant_line.get("spliceAI") != None: - splice_ai_line = variant_line["spliceAI"][0] # TODO I am making the huge assumption that we are only grabbing 1 - for vat_splice_ai_fieldname in splice_ai_fieldnames: # like "splice_ai_acceptor_gain_score" - nirvana_splice_ai_fieldname = vat_nirvana_splice_ai_dictionary.get(vat_splice_ai_fieldname) - splice_ai_fieldvalue = splice_ai_line.get(nirvana_splice_ai_fieldname) - row[vat_splice_ai_fieldname] = splice_ai_fieldvalue - - if variant_line.get("clinvar") != None: - clinvar_lines = variant_line["clinvar"] # TODO I am making the huge assumption that this is correctly pulling the RCV one - for clinvar_correct_line in clinvar_lines: - # get the clinvar line with the id that starts with RCV - if clinvar_correct_line.get("id")[:2] == "RCV": - for vat_clinvar_fieldname in clinvar_fieldnames: # like "clinvar_classification" - nirvana_clinvar_fieldname = vat_nirvana_clinvar_dictionary.get(vat_clinvar_fieldname) - clinvar_fieldvalue = clinvar_correct_line.get(nirvana_clinvar_fieldname) - row[vat_clinvar_fieldname] = clinvar_fieldvalue - - if variant_line.get("revel") != None: - row["revel"] = variant_line.get("revel").get("score") - - return row - -def make_annotated_row(row_position, variant_line, transcript_line): # would it be better to not pass the transcript_line since its dupe data? - positions_fieldnames, variants_fieldnames, transcripts_fieldnames, gvs_alleles_fieldnames, revel_fieldnames, splice_ai_fieldnames, clinvar_fieldnames, gnomad_fieldnames, omim_fieldnames = make_fieldnames() row = {} row["position"] = row_position # this is a required field -- do we want validation? (what about validation for all the variants_fieldnames?) @@ -198,7 +133,7 @@ def make_annotated_row(row_position, variant_line, transcript_line): # would it clinvar_lines = variant_line["clinvar"] # TODO I am making the huge assumption that this is correctly pulling the RCV one for clinvar_correct_line in clinvar_lines: # get the clinvar line with the id that starts with RCV - if clinvar_correct_line.get("id")[:2] == "RCV": + if clinvar_correct_line.get("id")[:2] == "RCV": # TODO, does this need to be 3, am I being a dummy here? for vat_clinvar_fieldname in clinvar_fieldnames: # like "clinvar_classification" nirvana_clinvar_fieldname = vat_nirvana_clinvar_dictionary.get(vat_clinvar_fieldname) clinvar_fieldvalue = clinvar_correct_line.get(nirvana_clinvar_fieldname) @@ -209,126 +144,13 @@ def make_annotated_row(row_position, variant_line, transcript_line): # would it return row -def make_annotation_tables(annotated_json): - variant_transcript_table_output_csv = "aou_alpha1_shard_annotations_vat.csv" # TODO get this from the annotated_json name - genes_output_csv = "aou_alpha1_shard_annotations_vat_genes.csv" # TODO get this from the annotated_json name - # make_variant_transcript_table(annotated_json, variant_transcript_table_output_csv) - make_genes_table(annotated_json, genes_output_csv) - -def make_genes_table(annotated_json, output_csv): # why is this taking so long? I think we will want the reading to be done as a single script to make both tables - with open(output_csv, 'w', newline='') as csvfile: - omim_fieldnames = list(vat_nirvana_omim_dictionary.keys()) - fieldnames = omim_fieldnames - fieldnames.extend(["gene_symbol","gene_omim_id"]) - writer = csv.DictWriter(csvfile, fieldnames=fieldnames) - writer.writeheader() - json_data = open(annotated_json) - data = json.load(json_data) - gene_lines = data["genes"] # we want to write this out elsewhere? - for gene_line in gene_lines: - if gene_line.get("omim") != None: - row = {} - row["gene_symbol"] = gene_line.get("name") # TODO throw an error if it's None? We dont care if there's no omim tho, right? right! cuz nothin would be there to add in the join - omim_line = gene_line["omim"][0] # TODO I am making the huge assumption that we are only grabbing 1 - row["gene_omim_id"] = omim_line.get("mimNumber") - - if omim_line.get("phenotypes") != None: - phenotypes_line = omim_line["phenotypes"][0] # TODO I am making the huge assumption that we are only grabbing 1 - for vat_omim_fieldname in omim_fieldnames: # like "mimNumber", "phenotype" - nirvana_omim_fieldname = vat_nirvana_omim_dictionary.get(vat_omim_fieldname) - omim_fieldvalue = phenotypes_line.get(nirvana_omim_fieldname) - row[vat_omim_fieldname] = omim_fieldvalue - writer.writerow(row) - -def make_variant_transcript_table(annotated_json, output_csv): - with open(output_csv, 'w', newline='') as csvfile: - positions_fieldnames, variants_fieldnames, transcripts_fieldnames, gvs_alleles_fieldnames, revel_fieldnames, splice_ai_fieldnames, clinvar_fieldnames, gnomad_fieldnames, omim_fieldnames = make_fieldnames() - fieldnames = positions_fieldnames - fieldnames.extend(variants_fieldnames) - fieldnames.extend(transcripts_fieldnames) - fieldnames.extend(gvs_alleles_fieldnames) - fieldnames.extend(revel_fieldnames) - fieldnames.extend(splice_ai_fieldnames) - fieldnames.extend(clinvar_fieldnames) - fieldnames.extend(gnomad_fieldnames) - # fieldnames.extend(omim_fieldnames) - writer = csv.DictWriter(csvfile, fieldnames=fieldnames) - - writer.writeheader() - # in the future can we simplify this pre-processing? - json_data = open(annotated_json) - data = json.load(json_data) - annotated_json_lines = data["positions"] - for annotated_json_line in annotated_json_lines: - row_position = annotated_json_line.get("position") # this is a required field -- do we want validation? - # want to write a csv row for each variant - transcript - # so let's start with each variant - variant_lines = annotated_json_line.get("variants") # this is a required field -- do we want validation? - for variant_line in variant_lines: - if variant_line.get("transcripts") == None: - # then we make a special row - row = make_annotated_row(row_position, variant_line, None) - writer.writerow(row) - else: - transcript_lines = variant_line.get("transcripts") - for transcript_line in transcript_lines: - row = make_annotated_row(row_position, variant_line, transcript_line) - writer.writerow(row) - - -def make_annotation_json(annotated_json, output_json): - output_file=open(output_json, 'w') - json_data = open(annotated_json, 'r') - data = json.load(json_data) - annotated_json_lines = data['positions'] - for annotated_json_line in annotated_json_lines: - position=annotated_json_line.get('position') - variants=annotated_json_line.get('variants') - for variant in variants: - make_variant_line={} # remember that we want one for each variant-transcript and variant-null for variants without transcripts - make_variant_line['position']=position - for value in vat_nirvana_variants_dictionary.values(): - make_variant_line[value]=variant.get(value) - if variant.get("revel") != None: # TODO check with Lee to see if this spacing is safe -- if there are no transcripts will there always never be a revel, spliceAT etc? - make_variant_line["revel"] = variant.get("revel").get("score") - if variant.get("spliceAI") != None: - spliceAI_first_item = variant.get("spliceAI")[0] - make_variant_line["spliceAI"]={} - for value in vat_nirvana_splice_ai_dictionary.values(): - make_variant_line["spliceAI"][value]=spliceAI_first_item.get(value) # TODO I am making the huge assumption that we are only grabbing the first - if variant.get("clinvar") != None: - clinvar_items = variant.get("clinvar") - make_variant_line["clinvar"]={} - for clinvar_item in clinvar_items: - if clinvar_item.get("id")[:3] == "RCV": # would it be better to save this processing for in BQ? - for value in vat_nirvana_clinvar_dictionary.values(): - make_variant_line["clinvar"][value]=clinvar_item.get(value) - if variant.get("gnomad") != None: - make_variant_line["gnomad"]={} - for value in vat_nirvana_gnomad_dictionary.values(): - make_variant_line["gnomad"][value]=variant.get("gnomad").get(value) - if variant.get("transcripts") == None: - back_json=json.dumps(make_variant_line) - output_file.write(back_json) - output_file.write("\n") - else: - transcript_lines = variant.get("transcripts") - for transcript_line in transcript_lines: - make_transcript_line=make_variant_line # remember that we want one for each variant-transcript and variant-null for variants without transcripts - for value in vat_nirvana_transcripts_dictionary.values(): - make_transcript_line[value]=transcript_line.get(value) - back_json=json.dumps(make_transcript_line) - output_file.write(back_json) - output_file.write("\n") - output_file.close() - -def make_annotation_json_better(annotated_json, output_json, output_genes_json): +def make_annotation_jsons(annotated_json, output_json, output_genes_json): output_file=open(output_json, 'w') output_genes_file=open(output_genes_json, 'w') json_data = open(annotated_json, 'r') data = json.load(json_data) annotated_position_lines = data['positions'] - annotated_gene_lines = data['genes'] + annotated_gene_lines = data['genes'] # Is there any reason to split up the genes and positions json creation into two helper scripts? for annotated_json_line in annotated_position_lines: position=annotated_json_line.get('position') # this is a required field -- do we want validation? variants=annotated_json_line.get('variants') @@ -370,14 +192,12 @@ def make_annotation_json_better(annotated_json, output_json, output_genes_json): """ if __name__ == '__main__': parser = argparse.ArgumentParser(allow_abbrev=False, description='Extract a cohort from BigQuery Variant Store ') - parser.add_argument('--fq_petvet_dataset',type=str, help='project.dataset location of pet/vet data', required=True) + parser.add_argument('--annotated_json',type=str, help='nirvana created annotation json', required=True) # Execute the parse_args() method args = parser.parse_args() - make_annotation_tables(annotated_json) """ + make_annotation_jsons(annotated_json, json_prefix) """ -#make_annotation_tables("ralpha1.json") -make_annotation_json_better("ralpha1.json", "aou_alpha1_shard_annotations_bq_load.json", "aou_alpha1_shard_genes_bq_load.json") -#make_annotation_json("ralpha1.json", "aou_alpha1_shard_annotations_bq_load.json") +make_annotation_jsons("ralpha1.json", "aou_alpha1_shard_annotations_bq_load.json", "aou_alpha1_shard_genes_bq_load.json") From 47f3b309c04038aa3c57f9024e2d806f58e61b09 Mon Sep 17 00:00:00 2001 From: rori <6863459+RoriCremer@users.noreply.github.com> Date: Fri, 25 Jun 2021 12:05:14 -0400 Subject: [PATCH 31/73] python cleanup --- .../create_variant_annotation_table.py | 45 ++++++++++--------- 1 file changed, 23 insertions(+), 22 deletions(-) diff --git a/scripts/variantstore/wdl/extract/create_variant_annotation_table.py b/scripts/variantstore/wdl/extract/create_variant_annotation_table.py index e2b44d04c65..000447663ec 100644 --- a/scripts/variantstore/wdl/extract/create_variant_annotation_table.py +++ b/scripts/variantstore/wdl/extract/create_variant_annotation_table.py @@ -3,13 +3,9 @@ import time import datetime -from google.cloud import bigquery -from google.cloud.bigquery.job import QueryJobConfig -from google.oauth2 import service_account - import csv import json - +import argparse JOB_IDS = set() @@ -98,43 +94,43 @@ def make_annotated_json_row(row_position, variant_line, transcript_line): # woul row = {} row["position"] = row_position # this is a required field -- do we want validation? (what about validation for all the variants_fieldnames?) - for vat_variants_fieldname in variants_fieldnames: # like "contig" + for vat_variants_fieldname in vat_nirvana_variants_dictionary.keys(): # like "contig" nirvana_variants_fieldname = vat_nirvana_variants_dictionary.get(vat_variants_fieldname) variant_fieldvalue = variant_line.get(nirvana_variants_fieldname) row[vat_variants_fieldname] = variant_fieldvalue if transcript_line != None: - for vat_transcripts_fieldname in transcripts_fieldnames: # like "transcript" + for vat_transcripts_fieldname in vat_nirvana_transcripts_dictionary.keys(): # like "transcript" nirvana_transcripts_fieldname = vat_nirvana_transcripts_dictionary.get(vat_transcripts_fieldname) transcript_fieldvalue = transcript_line.get(nirvana_transcripts_fieldname) if nirvana_transcripts_fieldname == "isCanonical" and transcript_fieldvalue != True: # oooof this is ugly transcript_fieldvalue = False row[vat_transcripts_fieldname] = transcript_fieldvalue - for vat_gvs_alleles_fieldname in gvs_alleles_fieldnames: # like "gvs_all_ac" + for vat_gvs_alleles_fieldname in vat_nirvana_gvs_alleles_dictionary.keys(): # like "gvs_all_ac" nirvana_gvs_alleles_fieldname = vat_nirvana_gvs_alleles_dictionary.get(vat_gvs_alleles_fieldname) gvs_alleles_fieldvalue = variant_line.get(nirvana_gvs_alleles_fieldname) row[vat_gvs_alleles_fieldname] = gvs_alleles_fieldvalue - if variant_line.get("gnomad") != None: - for vat_gnomad_fieldname in gnomad_fieldnames: # like "gnomad_all_af" - nirvana_gnomad_fieldname = vat_nirvana_gnomad_dictionary.get(vat_gnomad_fieldname) - gnomad_fieldvalue = variant_line.get("gnomad").get(nirvana_gnomad_fieldname) # not a list like the others - row[vat_gnomad_fieldname] = gnomad_fieldvalue - if variant_line.get("spliceAI") != None: splice_ai_line = variant_line["spliceAI"][0] # TODO I am making the huge assumption that we are only grabbing 1 - for vat_splice_ai_fieldname in splice_ai_fieldnames: # like "splice_ai_acceptor_gain_score" + for vat_splice_ai_fieldname in vat_nirvana_splice_ai_dictionary.keys(): # like "splice_ai_acceptor_gain_score" nirvana_splice_ai_fieldname = vat_nirvana_splice_ai_dictionary.get(vat_splice_ai_fieldname) splice_ai_fieldvalue = splice_ai_line.get(nirvana_splice_ai_fieldname) row[vat_splice_ai_fieldname] = splice_ai_fieldvalue + if variant_line.get("gnomad") != None: + for vat_gnomad_fieldname in vat_nirvana_gnomad_dictionary.keys(): # like "gnomad_all_af" + nirvana_gnomad_fieldname = vat_nirvana_gnomad_dictionary.get(vat_gnomad_fieldname) + gnomad_fieldvalue = variant_line.get("gnomad").get(nirvana_gnomad_fieldname) # not a list like the others + row[vat_gnomad_fieldname] = gnomad_fieldvalue + if variant_line.get("clinvar") != None: clinvar_lines = variant_line["clinvar"] # TODO I am making the huge assumption that this is correctly pulling the RCV one for clinvar_correct_line in clinvar_lines: # get the clinvar line with the id that starts with RCV if clinvar_correct_line.get("id")[:2] == "RCV": # TODO, does this need to be 3, am I being a dummy here? - for vat_clinvar_fieldname in clinvar_fieldnames: # like "clinvar_classification" + for vat_clinvar_fieldname in vat_nirvana_clinvar_dictionary.keys(): # like "clinvar_classification" nirvana_clinvar_fieldname = vat_nirvana_clinvar_dictionary.get(vat_clinvar_fieldname) clinvar_fieldvalue = clinvar_correct_line.get(nirvana_clinvar_fieldname) row[vat_clinvar_fieldname] = clinvar_fieldvalue @@ -187,17 +183,22 @@ def make_annotation_jsons(annotated_json, output_json, output_genes_json): row[vat_omim_fieldname] = omim_fieldvalue back_json=json.dumps(row) output_genes_file.write(back_json) - aou_shard_223_vatteroutput_genes_file.write("\n") + output_genes_file.write("\n") output_genes_file.close() -""" if __name__ == '__main__': - parser = argparse.ArgumentParser(allow_abbrev=False, description='Extract a cohort from BigQuery Variant Store ') +if __name__ == '__main__': + parser = argparse.ArgumentParser(allow_abbrev=False, description='Create BQ load friendly jsons for VAT creation') parser.add_argument('--annotated_json',type=str, help='nirvana created annotation json', required=True) - + parser.add_argument('--output_vt_json',type=str, help='name of the vt json', required=True) + parser.add_argument('--output_genes_json',type=str, help='name of the genes json', required=True) # Execute the parse_args() method args = parser.parse_args() - make_annotation_jsons(annotated_json, json_prefix) """ + make_annotation_jsons(args.annotated_json, + args.output_vt_json, + args.output_genes_json) -make_annotation_jsons("ralpha1.json", "aou_alpha1_shard_annotations_bq_load.json", "aou_alpha1_shard_genes_bq_load.json") +#make_annotation_jsons("ralpha1.json", "aou_alpha1_shard_annotations_bq_load.json", "aou_alpha1_shard_genes_bq_load.json") +# TODO add this to the ah_var_store docker!!! +# TODO do I want to gsutil cp up the files into a bucket here? \ No newline at end of file From 2294c520cb42415f1a5bf23b7e02620d2e91a0d5 Mon Sep 17 00:00:00 2001 From: rori <6863459+RoriCremer@users.noreply.github.com> Date: Tue, 29 Jun 2021 10:45:31 -0400 Subject: [PATCH 32/73] more vars for the wdl --- .../variantstore/wdl/GvsSitesOnlyVCF.example.inputs.json | 7 +++++-- 1 file changed, 5 insertions(+), 2 deletions(-) diff --git a/scripts/variantstore/wdl/GvsSitesOnlyVCF.example.inputs.json b/scripts/variantstore/wdl/GvsSitesOnlyVCF.example.inputs.json index d8101d0f26e..8f42fefaac1 100644 --- a/scripts/variantstore/wdl/GvsSitesOnlyVCF.example.inputs.json +++ b/scripts/variantstore/wdl/GvsSitesOnlyVCF.example.inputs.json @@ -1,11 +1,14 @@ { - "GvsSitesOnlyVCF.gvs_extract_cohort_filtered_vcfs": ["gs://broad-dsp-spec-ops/kcibul/ft/gvs.chr20.vcf.gz", "gs://broad-dsp-spec-ops/scratch/rcremer/Nirvana/Data/gvs_features_0.vcf.gz"], - "GvsSitesOnlyVCF.gvs_extract_cohort_filtered_vcf_indices": ["gs://broad-dsp-spec-ops/kcibul/ft/gvs.chr20.vcf.gz.tbi", "gs://broad-dsp-spec-ops/scratch/rcremer/Nirvana/Data/gvs_features_0.vcf.gz.tbi"], + "GvsSitesOnlyVCF.gvs_extract_cohort_filtered_vcfs": ["gs://fc-secure-daa074a0-884f-4b67-a79b-cb5cd1556c9f/e73809fa-9ef2-4f3b-965c-846eff4b905e/GvsExtractCallset/48c56780-2520-444f-b1b3-83091a74bb08/call-ExtractTask/shard-223/alpha1_1000_223.vcf.gz", "gs://fc-secure-daa074a0-884f-4b67-a79b-cb5cd1556c9f/e73809fa-9ef2-4f3b-965c-846eff4b905e/GvsExtractCallset/48c56780-2520-444f-b1b3-83091a74bb08/call-ExtractTask/shard-0/alpha1_1000_0.vcf.gz"], + "GvsSitesOnlyVCF.gvs_extract_cohort_filtered_vcf_indices": ["gs://fc-secure-daa074a0-884f-4b67-a79b-cb5cd1556c9f/e73809fa-9ef2-4f3b-965c-846eff4b905e/GvsExtractCallset/48c56780-2520-444f-b1b3-83091a74bb08/call-ExtractTask/shard-223/alpha1_1000_223.vcf.gz.tbi", "gs://fc-secure-daa074a0-884f-4b67-a79b-cb5cd1556c9f/e73809fa-9ef2-4f3b-965c-846eff4b905e/GvsExtractCallset/48c56780-2520-444f-b1b3-83091a74bb08/call-ExtractTask/shard-0/alpha1_1000_0.vcf.gz.tbi"], "GvsSitesOnlyVCF.output_sites_only_file_name": "hello_did_I_sites_only", "GvsSitesOnlyVCF.output_merged_file_name": "hello_did_I_merge", "GvsSitesOnlyVCF.output_annotated_file_name": "hello_did_I_annotate", "GvsSitesOnlyVCF.nirvana_data_directory": "gs://broad-dsp-spec-ops/scratch/rcremer/Nirvana/NirvanaData.tar.gz", "GvsSitesOnlyVCF.nirvana_schema_json_file": "gs://broad-dsp-spec-ops/scratch/rcremer/Nirvana/schemas/vat_schema.json", + "GvsSitesOnlyVCF.vat_vt_schema_json_file": "gs://broad-dsp-spec-ops/scratch/rcremer/Nirvana/schemas/vt_schema.json", + "GvsSitesOnlyVCF.nirvana_override_json": "gs://broad-dsp-spec-ops/scratch/rcremer/Nirvana/hello_did_I_annotate.json", + "GvsSitesOnlyVCF.create_vat_jsons_python_script": "gs://broad-dsp-spec-ops/scratch/rcremer/Nirvana/create_vat_jsons_python_script.py", "GvsSitesOnlyVCF.project_id": "spec-ops-aou", "GvsSitesOnlyVCF.dataset_name": "anvil_100_for_testing" } From 68846ae1a1c40030e3ade9d563e1f27bd8a663ad Mon Sep 17 00:00:00 2001 From: rori <6863459+RoriCremer@users.noreply.github.com> Date: Tue, 29 Jun 2021 10:46:00 -0400 Subject: [PATCH 33/73] still need to get the right array info --- scripts/variantstore/wdl/schemas/vat_genes_schema.json | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/scripts/variantstore/wdl/schemas/vat_genes_schema.json b/scripts/variantstore/wdl/schemas/vat_genes_schema.json index bdefadf854d..fba7027d13a 100644 --- a/scripts/variantstore/wdl/schemas/vat_genes_schema.json +++ b/scripts/variantstore/wdl/schemas/vat_genes_schema.json @@ -20,7 +20,7 @@ { "description": "OMIM Disease Name TODO -- this needs to be swapped to Repeated not nullable and String not Integer?", "name": "omim_phenotypes_name", -"type": "Integer", +"type": "String", "mode": "Nullable" } ] \ No newline at end of file From 876716ec66b21a2fe36159f1360d6605ecbe1539 Mon Sep 17 00:00:00 2001 From: rori <6863459+RoriCremer@users.noreply.github.com> Date: Tue, 29 Jun 2021 10:46:25 -0400 Subject: [PATCH 34/73] vat should be all the cols from Lee --- .../variantstore/wdl/schemas/vat_schema.json | 18 ++++++++++++++++++ 1 file changed, 18 insertions(+) diff --git a/scripts/variantstore/wdl/schemas/vat_schema.json b/scripts/variantstore/wdl/schemas/vat_schema.json index a2c93726ed8..65789af26f6 100644 --- a/scripts/variantstore/wdl/schemas/vat_schema.json +++ b/scripts/variantstore/wdl/schemas/vat_schema.json @@ -244,5 +244,23 @@ "name": "gnomad_max_subpop", "type": "INTEGER", "mode": "Nullable" + }, + { + "description": "OMIM ID", + "name": "gene_omim_id", + "type": "Integer", + "mode": "Nullable" + }, + { + "description": "OMIM Disease ID TODO -- this needs to be swapped to Repeated not nullable", + "name": "omim_phenotypes_id", + "type": "Integer", + "mode": "Nullable" + }, + { + "description": "OMIM Disease Name TODO -- this needs to be swapped to Repeated not nullable?", + "name": "omim_phenotypes_name", + "type": "String", + "mode": "Nullable" } ] From deb9c3b09388f377af4d76ca472328d7cd442035 Mon Sep 17 00:00:00 2001 From: rori <6863459+RoriCremer@users.noreply.github.com> Date: Tue, 29 Jun 2021 10:47:08 -0400 Subject: [PATCH 35/73] add initial validation to wdl --- scripts/variantstore/wdl/GvsSitesOnlyVCF.wdl | 527 +++++++++++++------ 1 file changed, 360 insertions(+), 167 deletions(-) diff --git a/scripts/variantstore/wdl/GvsSitesOnlyVCF.wdl b/scripts/variantstore/wdl/GvsSitesOnlyVCF.wdl index 0734c3beff9..c287d67e13d 100644 --- a/scripts/variantstore/wdl/GvsSitesOnlyVCF.wdl +++ b/scripts/variantstore/wdl/GvsSitesOnlyVCF.wdl @@ -1,66 +1,74 @@ version 1.0 workflow GvsSitesOnlyVCF { # tested with "gs://broad-dsp-spec-ops/scratch/rcremer/Nirvana/Data/anvil_expected.vcf" input { - Array[File] gvs_extract_cohort_filtered_vcfs # gonna try this one next: gs://broad-dsp-spec-ops/kcibul/ft/gvs.chr20.vcf.gz, - Array[File] gvs_extract_cohort_filtered_vcf_indices # gonna try this one next: gs://broad-dsp-spec-ops/kcibul/ft/gvs.chr20.vcf.gz, + Array[File] gvs_extract_cohort_filtered_vcfs + Array[File] gvs_extract_cohort_filtered_vcf_indices String output_sites_only_file_name String output_merged_file_name String output_annotated_file_name String project_id String dataset_name File nirvana_data_directory + File nirvana_override_json File nirvana_schema_json_file - String? genes_vat_schema = "gene_symbol:STRING,gene_omim_id:INTEGER,omim_phenotypes_id:INTEGER,omim_phenotypes_name:STRING" + File vat_vt_schema_json_file + File create_vat_jsons_python_script + String genes_vat_schema = "gene_symbol:STRING,gene_omim_id:INTEGER,omim_phenotypes_id:INTEGER,omim_phenotypes_name:INTEGER" File? gatk_override } - scatter(i in range(length(gvs_extract_cohort_filtered_vcfs)) ) { - call SitesOnlyVcf { - input: - vcf_bgz_gts = gvs_extract_cohort_filtered_vcfs[i], - vcf_index = gvs_extract_cohort_filtered_vcf_indices[i], - output_filename = "${output_sites_only_file_name}_${i}.sites_only.vcf.gz", - } + # TODO need to decide where to specify the name of the VAT table now that it is needed in 2 steps: BigQueryLoadJson and BigQuerySmokeTest <-- should these be one step? + + #scatter(i in range(length(gvs_extract_cohort_filtered_vcfs)) ) { + scatter(i in range(length(["1"])) ) { + #call SitesOnlyVcf { + # input: + # vcf_bgz_gts = gvs_extract_cohort_filtered_vcfs[i], + # vcf_index = gvs_extract_cohort_filtered_vcf_indices[i], + # output_filename = "${output_sites_only_file_name}_${i}.sites_only.vcf.gz", + #} + + #call AnnotateShardedVCF { + # input: + # input_vcf = SitesOnlyVcf.output_vcf, + # input_vcf_index = SitesOnlyVcf.output_vcf_idx, + # output_annotated_file_name = "${output_annotated_file_name}_${i}", + # nirvana_data_tar = nirvana_data_directory + #} + + call PrepAnnotationJson { + input: + # annotation_json = AnnotateShardedVCF.annotation_json, + annotation_json = nirvana_override_json, + python_script = create_vat_jsons_python_script, + output_name = "${i}.json" + } + + call BucketJson { # TODO should this be it's own step? We are just gsutiling + input: + vt_bq_loading_json = PrepAnnotationJson.vat_vt_json, + genes_bq_loading_json = PrepAnnotationJson.vat_genes_json + } } - call MergeVCFs { # why are we merging before annotating? couldn't we keep them separate? - # I guess if we create the table in one single thread, we can load data w multi (we would be downloading the annotations many times perhaps...) - input: - input_vcfs = SitesOnlyVcf.output_vcf, - input_vcf_indices = SitesOnlyVcf.output_vcf_idx, - output_merged_file_name = output_merged_file_name, - } - - call AnnotateVCF { - input: - input_vcf = MergeVCFs.merged_vcf, - output_annotated_file_name = output_annotated_file_name, - nirvana_data_tar = nirvana_data_directory - } - #call AnnotateShardedVCF { - # input: - # input_vcfs = SitesOnlyVcf.output_vcf, - # output_annotated_file_name = output_annotated_file_name, - # nirvana_data_tar = nirvana_data_directory - #} - - # call PrepAnnotationJson { # TODO should this be it's own step? We need to run a python script to prep the jsons for bq - # input: - # annotation_json = AnnotateVCF.annotation_json, - # } - - # call BigQueryLoadJson { # If we dont use the above step to prep w a python script-- we are assuming BQ docker has python - # input: - # annotation_json = AnnotateVCF.annotation_json, - # #annotation_json_jsi = AnnotateVCF.annotation_json_jsi - # nirvana_schema = nirvana_schema_json_file, - # project_id = project_id, - # dataset_name = dataset_name - # } + call BigQueryLoadJson { + input: + nirvana_schema = nirvana_schema_json_file, + vt_schema = vat_vt_schema_json_file, + genes_schema = genes_vat_schema, + project_id = project_id, + dataset_name = dataset_name + } + + call BigQuerySmokeTest { + input: + project_id = project_id, + dataset_name = dataset_name, + # annotation_json = AnnotateShardedVCF.annotation_json + annotation_json = nirvana_override_json + } } - - ################################################################################ task SitesOnlyVcf { input { @@ -94,46 +102,14 @@ task SitesOnlyVcf { } } -task MergeVCFs { - input { - Array[File] input_vcfs - Array[File] input_vcf_indices - String output_merged_file_name - } - # TODO Ideally we wouldn't merge the vcfs at all, but keep them separated by position - # and then annotate them separately and then load each of the annotation.jsons into BQ (may involve multiple temp tables that each get mapped to the final vat) - - String output_vcf = basename(output_merged_file_name) + ".vcf.gz" - String output_vcf_idx = basename(output_vcf) + ".tbi" - command <<< - set -e - gatk --java-options "-Xmx2048m" \ - MergeVcfs -I ~{sep=' -I ' input_vcfs} -O ~{output_vcf} - - >>> - # ------------------------------------------------ - # Runtime settings: - runtime { - docker: "broadinstitute/gatk:4.2.0.0" - memory: "3 GB" - cpu: "1" - disks: "local-disk 100 HDD" - } - # ------------------------------------------------ - # Outputs: - output { - File merged_vcf = "~{output_vcf}" - File merged_vcf_idx = "~{output_vcf_idx}" - } -} - task AnnotateShardedVCF { input { - Array[File] input_vcfs + File input_vcf + File input_vcf_index String output_annotated_file_name File nirvana_data_tar } - String annotation_json_name = basename(output_annotated_file_name) + ".json.gz" + String annotation_json_name = output_annotated_file_name + ".json.gz" String annotation_json_name_jsi = annotation_json_name + ".jsi" String nirvana_location = "/opt/nirvana/Nirvana.dll" @@ -153,17 +129,13 @@ task AnnotateShardedVCF { tar zxvf ~{nirvana_data_tar} -C datasources_dir --strip-components 2 DATA_SOURCES_FOLDER="$PWD/datasources_dir" - # do a bash loop here to single thread annotate each of the files in the array - for input_vcf in input_vcfs - do - dotnet ~{nirvana_location} \ + dotnet ~{nirvana_location} \ -c $DATA_SOURCES_FOLDER~{path} \ --sd $DATA_SOURCES_FOLDER~{path_supplementary_annotations} \ -r $DATA_SOURCES_FOLDER~{path_reference} \ - -i ~{input_vcfs} \ - -o ~{output_annotated_file_name+"input_vcf letter or Ii or somethinig?"} - done + -i ~{input_vcf} \ + -o ~{output_annotated_file_name} >>> @@ -171,8 +143,8 @@ task AnnotateShardedVCF { # Runtime settings: runtime { docker: "annotation/nirvana:3.14" # this download is too slow---can we beef this up? - memory: "3 GB" - cpu: "1" + memory: "5 GB" + cpu: "2" disks: "local-disk 100 HDD" } # ------------------------------------------------ @@ -183,60 +155,109 @@ task AnnotateShardedVCF { } } -task AnnotateVCF { # can we add the tar to the docker container? +task PrepAnnotationJsonJQ { input { - File input_vcf - String output_annotated_file_name - File nirvana_data_tar + File annotation_json + File python_script + String output_name } - String annotation_json_name = basename(output_annotated_file_name) + ".json.gz" - String annotation_json_name_jsi = annotation_json_name + ".jsi" - String nirvana_location = "/opt/nirvana/Nirvana.dll" - String path = "/Cache/GRCh38/Both" - String path_supplementary_annotations = "/SupplementaryAnnotation/GRCh38" - String path_reference = "/References/Homo_sapiens.GRCh38.Nirvana.dat" + String output_vt_json = "vat_vt_bq_load" + output_name + String output_genes_json = "vat_genes_bq_load" + output_name command <<< set -e - # NOTE: Validate a lil so that we don't waste time copying down the data sources if there's an error. - # ======================================= - # Handle our data sources: + python ~{python_script} \ + --annotated_json ~{annotation_json} \ + --output_vt_json ~{output_vt_json} \ + --output_genes_json ~{output_genes_json} - # Extract the tar.gz: - echo "Extracting annotation data sources tar/gzip file..." - mkdir datasources_dir - tar zxvf ~{nirvana_data_tar} -C datasources_dir --strip-components 2 - DATA_SOURCES_FOLDER="$PWD/datasources_dir" + >>> + # ------------------------------------------------ + # Runtime settings: + runtime { + docker: "us.gcr.io/broad-dsde-methods/variantstore-export:091920" + memory: "10 GB" + cpu: "2" + disks: "local-disk 100 HDD" + } + # ------------------------------------------------ + # Outputs: + output { + File vat_vt_json="~{output_vt_json}" + File vat_genes_json="~{output_genes_json}" + } +} - dotnet ~{nirvana_location} \ - -c $DATA_SOURCES_FOLDER~{path} \ - --sd $DATA_SOURCES_FOLDER~{path_supplementary_annotations} \ - -r $DATA_SOURCES_FOLDER~{path_reference} \ - -i ~{input_vcf} \ - -o ~{output_annotated_file_name} - >>> +task PrepAnnotationJson { + input { + File annotation_json + File python_script + String output_name + } + + String output_vt_json = "vat_vt_bq_load" + output_name + String output_genes_json = "vat_genes_bq_load" + output_name + + command <<< + set -e + + python ~{python_script} \ + --annotated_json ~{annotation_json} \ + --output_vt_json ~{output_vt_json} \ + --output_genes_json ~{output_genes_json} + + >>> # ------------------------------------------------ # Runtime settings: runtime { - docker: "annotation/nirvana:3.14" # this download is too slow---can we beef this up? - memory: "3 GB" + docker: "us.gcr.io/broad-dsde-methods/variantstore-export:091920" + memory: "10 GB" + cpu: "2" + disks: "local-disk 100 HDD" + } + # ------------------------------------------------ + # Outputs: + output { + File vat_vt_json="~{output_vt_json}" + File vat_genes_json="~{output_genes_json}" + } +} + +task BucketJson { + input { + File vt_bq_loading_json + File genes_bq_loading_json + } + + command <<< + set -e + + gsutil cp ~{vt_bq_loading_json} gs://broad-dsp-spec-ops/scratch/rcremer/Nirvana/output/vt/ + gsutil cp ~{genes_bq_loading_json} gs://broad-dsp-spec-ops/scratch/rcremer/Nirvana/output/genes/ + + >>> + # ------------------------------------------------ + # Runtime settings: + runtime { + docker: "google/cloud-sdk:latest" + memory: "1 GB" cpu: "1" disks: "local-disk 100 HDD" } # ------------------------------------------------ # Outputs: output { - File annotation_json = "~{annotation_json_name}" - File annotation_json_jsi = "~{annotation_json_name_jsi}" + Boolean done = true } } task BigQueryLoadJson { input { - File annotation_json File nirvana_schema + File vt_schema + String genes_schema String project_id String dataset_name } @@ -244,59 +265,72 @@ task BigQueryLoadJson { # I am going to want to have two pre-vat tables. A variant table and a genes table. They will be joined together for the vat table # See if we can grab the annotations json directly from the gcp bucket (so pull it in as a string so it wont) - String vat_table = "vatter" + String vat_table = "vat_jun28" String variant_transcript_table = "vat_vt" String genes_table = "vat_genes" - # instead of the annotation_json we now need two jsons which are created from the annotation_json with a python script - # TODO run that python script on the annotation_json - # we will also want specific schemas for each of these tables---right now we are over-using one. Let's get Lee's sign off on the final one - File variant_transcript_bq_load.json = annotation_json - File genes_bq_load.json = annotation_json + # TODO there needs to be a LOOP somewhere give that there are now many files in GCP that need to be loaded into BQ + + String vt_jsons_path = "gs://broad-dsp-spec-ops/scratch/rcremer/Nirvana/output/vt/*" + String genes_jsons_path = "gs://broad-dsp-spec-ops/scratch/rcremer/Nirvana/output/genes/*" command <<< - set -e - # load the annotation json in as a temp interim BQ vat table - # TODO make sure when you load---if you split in some way, that you dont drop "header lines" from secondary shards that have no headers + bq show --project_id ~{project_id} ~{dataset_name}.~{variant_transcript_table} > /dev/null + BQ_SHOW_RC=$? - # since we expect to add to these tables, --replace=true is not a flag we want. Verify that this will not be loaded with a bq * - echo "Creating a pre-vat table ~{dataset_name}.~{variant_transcript_table}" - bq --location=US load --project_id=~{project_id} --source_format=NEWLINE_DELIMITED_JSON --autodetect ~{dataset_name}.~{variant_transcript_table} ~{variant_transcript_bq_load.json} - # bq --location=US load --replace=true --project_id="spec-ops-aou" --source_format=NEWLINE_DELIMITED_JSON --autodetect "anvil_100_for_testing.temp" /Users/aurora/Desktop/repositories/gatk/hello_did_I_annotate.json + set -e - echo "Creating a pre-vat table ~{dataset_name}.~{genes_table}" - bq --location=US load --project_id=~{project_id} --source_format=NEWLINE_DELIMITED_JSON --autodetect ~{dataset_name}.~{genes_table} ~{genes_bq_load.json} + if [ $BQ_SHOW_RC -ne 0 ]; then + echo "Creating a pre-vat table ~{dataset_name}.~{variant_transcript_table}" + bq --location=US mk --project_id=~{project_id} ~{dataset_name}.~{variant_transcript_table} ~{vt_schema} + fi - set +e - bq show --project_id ~{project_id} ~{dataset_name}.~{vat_table} > /dev/null - BQ_SHOW_RC=$? - set -e - if [ $BQ_SHOW_RC -ne 0 ]; then - echo "Creating the vat table ~{dataset_name}.~{vat_table}" - bq --location=US mk --project_id=~{project_id} ~{dataset_name}.~{vat_table} ~{nirvana_schema} - fi + echo "Loading data into a pre-vat table ~{dataset_name}.~{variant_transcript_table}" + # bq --location=US load --project_id=~{project_id} --source_format=NEWLINE_DELIMITED_JSON ~{dataset_name}.~{variant_transcript_table} ~{vt_jsons_path} + bq --location=US load --project_id="spec-ops-aou" --source_format=NEWLINE_DELIMITED_JSON "anvil_100_for_testing.vat_vt" gs://broad-dsp-spec-ops/scratch/rcremer/Nirvana/output/vt/* + set +e - # create the final vat table with the correct fields - PARTITION_FIELD="position" - CLUSTERING_FIELD="vid" - PARTITION_STRING="" #--range_partitioning=$PARTITION_FIELD,0,4000,4000" - CLUSTERING_STRING="" #--clustering_fields=$CLUSTERING_FIELD" + bq show --project_id ~{project_id} ~{dataset_name}.~{genes_table} > /dev/null + BQ_SHOW_RC=$? - set +e - bq show --project_id ~{project_id} ~{dataset_name}.~{vat_table} > /dev/null - BQ_SHOW_RC=$? - set -e - if [ $BQ_SHOW_RC -ne 0 ]; then - echo "Creating the vat table ~{dataset_name}.~{vat_table}" - bq --location=US mk --project_id=~{project_id} ~{dataset_name}.~{vat_table} ~{nirvana_schema} - fi + set -e + + if [ $BQ_SHOW_RC -ne 0 ]; then + echo "Creating a pre-vat table ~{dataset_name}.~{genes_table}" + bq --location=US mk --project_id=~{project_id} ~{dataset_name}.~{genes_table} ~{genes_schema} + fi + + echo "Loading data into a pre-vat table ~{dataset_name}.~{genes_table}" + # bq --location=US load --project_id=~{project_id} --source_format=NEWLINE_DELIMITED_JSON ~{dataset_name}.~{genes_table} ~{genes_jsons_path} + bq --location=US load --project_id=~{project_id} --source_format=NEWLINE_DELIMITED_JSON ~{dataset_name}.~{genes_table} gs://broad-dsp-spec-ops/scratch/rcremer/Nirvana/output/genes/* - echo "And putting data into it" + # create the final vat table with the correct fields + PARTITION_FIELD="position" + CLUSTERING_FIELD="vid" + PARTITION_STRING="" #--range_partitioning=$PARTITION_FIELD,0,4000,4000" + CLUSTERING_STRING="" #--clustering_fields=$CLUSTERING_FIELD" - # now run some giant query in BQ to get this all in the right table - bq query --nouse_legacy_sql --destination_table=~{dataset_name}.~{vat_table} --project_id=~{project_id} \ + set +e + + bq show --project_id ~{project_id} ~{dataset_name}.~{vat_table} > /dev/null + BQ_SHOW_RC=$? + + set -e + + # TODO check the below logic. Seems to be appending.....? + if [ $BQ_SHOW_RC -ne 0 ]; then + echo "Creating the vat table ~{dataset_name}.~{vat_table}" + bq --location=US mk --project_id=~{project_id} ~{dataset_name}.~{vat_table} ~{nirvana_schema} + else + bq rm -t -f --project_id=~{project_id} ~{dataset_name}.~{vat_table} + bq --location=US mk --project_id=~{project_id} ~{dataset_name}.~{vat_table} ~{nirvana_schema} + fi + echo "And putting data into it" + + # now run some giant query in BQ to get this all in the right table + bq query --nouse_legacy_sql --destination_table=~{dataset_name}.~{vat_table} --project_id=~{project_id} \ 'SELECT v.vid, v.transcript, @@ -310,19 +344,19 @@ task BigQueryLoadJson { v.gene_symbol, v.transcript_source, v.aa_change, - ARRAY_TO_STRING(v.consequence, ",") AS consequence, + v.consequence, #ARRAY_TO_STRING(v.consequence, ",") AS consequence, v.dna_change, v.variant_type, v.exon_number, v.intron_number, v.genomic_location, #v.hgvsc AS splice_distance has not yet been designed - ARRAY_TO_STRING(v.dbsnp_rsid, ",") AS dbsnp_rsid, + v.dbsnp_rsid, #ARRAY_TO_STRING(v.dbsnp_rsid, ",") AS dbsnp_rsid, v.entrez_gene_id, #g.hgnc_gene_id is not produced by Nirvana annotations g.gene_omim_id, CASE WHEN ( v.transcript is not null and v.is_canonical_transcript is not True) - THEN "false" WHEN ( v.transcript is not null and v.is_canonical_transcript is True) THEN "true" END AS is_canonical_transcript, + THEN False WHEN ( v.transcript is not null and v.is_canonical_transcript is True) THEN True END AS is_canonical_transcript, v.gnomad_all_af, v.gnomad_all_ac, v.gnomad_all_an, @@ -345,19 +379,178 @@ task BigQueryLoadJson { v.clinvar_classification, # validate that we only grab lines WHERE id LIKE "RCV%" v.clinvar_last_updated, v.clinvar_phenotype, - from `~{dataset_name}.~{variant_transcript_table}` as v + FROM `~{dataset_name}.~{variant_transcript_table}` as v left join `~{dataset_name}.~{genes_table}` as g on v.gene_symbol = g.gene_symbol' - # cat status_bq_submission | tail -n 1 > status_bq_submission_last_line - # bq_job_id=$(sed 's/.*://' status_bq_submission_last_line) - #echo $bq_job_id + # TODO why do I sometimes hit an error above, but still make it to the smoke test? + >>> + # ------------------------------------------------ + # Runtime settings: + runtime { + docker: "openbridge/ob_google-bigquery:latest" + memory: "3 GB" + cpu: "1" + disks: "local-disk 100 HDD" + } + # ------------------------------------------------ + # Outputs: + output { + Boolean done = true + } +} + +task BigQuerySmokeTest { + input { + String project_id + String dataset_name + File annotation_json + } + + # What I want to do here is query the final table for my expected results + # This will be hardcoded for now, but in the future I may want to pull a line out of the annotations json and use thats + + String vat_table = "vat_jun26" # TODO seems dangerous to specify this twice + + command <<< + set -e + + # validate the VAT table + echo "Does this table row look like I expect it to?" + # We will pass, or fail, a pipeline run by checking the following + + # ------------------------------------------------ + # VALIDATION #1 + # The number of passing variants in GVS matches the number of variants in the VAT. + # TODO this tests the python---what other qs should we ask here? + echo "VALIDATION #1" + # Please note that we are counting the number of variants in GVS, not the number of sites, which may add a difficulty to this task. + # TODO should these get broken down more so as not to test my sloppy bash over testing the data? + # TODO should I write this test in python instead?!?!? + # grep -o -i '"vid":' ~{annotation_json} | wc -l + ANNOTATE_JSON_VARIANT_COUNT=$(grep -o -i '"vid":' ~{annotation_json} | wc -l) + echo $ANNOTATE_JSON_VARIANT_COUNT + bq query --nouse_legacy_sql --project_id=~{project_id} 'SELECT COUNT (DISTINCT vid) FROM `~{dataset_name}.~{vat_table}`' + BQ_VAT_VARIANT_COUNT=$(bq query --nouse_legacy_sql --project_id=~{project_id} 'SELECT COUNT (DISTINCT vid) AS count FROM `~{dataset_name}.~{vat_table}`'| tr -dc '0-9') + echo $BQ_VAT_VARIANT_COUNT + + if [[ $ANNOTATE_JSON_VARIANT_COUNT -ne $BQ_VAT_VARIANT_COUNT ]] + then + echo "The number of variants is incorrect" + echo "Validation has failed" + exit 1 + else + echo "The number of passing variants in GVS matches the number of variants in the VAT" + fi + + # ------------------------------------------------ + # VALIDATION #2 + # Less than 5% of the variants have a non-null value in the gene field + echo "VALIDATION #2" + # Get the number of variants which have been joined (TODO is it the actual joining? or just the potential?) + bq query --nouse_legacy_sql --project_id=~{project_id} \ + 'SELECT COUNT (DISTINCT vid) AS count FROM `~{dataset_name}.~{vat_table}` WHERE gene_symbol IS NOT NULL' + BQ_VAT_GENE_COUNT=$(bq query --nouse_legacy_sql --project_id=~{project_id} 'SELECT COUNT (DISTINCT vid) AS count FROM `~{dataset_name}.~{vat_table}` WHERE gene_symbol IS NOT NULL'| tr -dc '0-9') + echo $BQ_VAT_GENE_COUNT + echo "Get the percent" + PERCENT=$((BQ_VAT_GENE_COUNT * 100 / BQ_VAT_VARIANT_COUNT)) + echo $PERCENT + + if [[ $PERCENT -gt 5 ]] + then echo "There are too many genes" + echo "Validation has failed" + # exit 1 <-- great! This worked! But need to get by it with my sloppy test data for now! + else + echo "Less than 5% of the variants have a non-null value in the gene field" + fi + + # ------------------------------------------------ + # VALIDATION #3 + # All variants in the TESK2 gene region (chr1:45,343,883-45,491,163) list multiple genes and those genes are always TESK2 and AL451136.1. + echo "VALIDATION #3" + # TODO ask Lee for help here. I'm not sure how to do this one? + # 'SELECT COUNT (DISTINCT vid) AS distinct_vid_count FROM `~{dataset_name}.~{vat_table}` WHERE contig="chr1"' + echo "Still need to validate chr1" + + # TODO this is not done! + + # ------------------------------------------------ + # VALIDATION #4 + # If a vid has a null transcript, then the vid is only in one row of the VAT. + echo "VALIDATION #4" + # Get a count of all the rows in the vat with no transcript + # Get a count of all distinct VID in vat with no transcript + # Make sure they are the same + # TODO we could in the future specify which VIDs are not distinct + bq query --nouse_legacy_sql --project_id=~{project_id} \ + 'SELECT COUNT (DISTINCT vid) AS distinct_vid_count FROM `~{dataset_name}.~{vat_table}` WHERE transcript IS NULL' + BQ_VAT_ROWS_NO_TRANSCRIPT_COUNT=$(bq query --nouse_legacy_sql --project_id=~{project_id} 'SELECT COUNT (DISTINCT vid) AS distinct_vid_count FROM `~{dataset_name}.~{vat_table}` WHERE transcript IS NULL'| tr -dc '0-9') + bq query --nouse_legacy_sql --project_id=~{project_id} \ + 'SELECT COUNT(*) AS count FROM `~{dataset_name}.~{vat_table}` WHERE transcript IS NULL' + BQ_VAT_VARIANT_NO_TRANSCRIPT_COUNT=$(bq query --nouse_legacy_sql --project_id=~{project_id} 'SELECT COUNT(*) AS count FROM `~{dataset_name}.~{vat_table}` WHERE transcript IS NULL'| tr -dc '0-9') + + echo $BQ_VAT_ROWS_NO_TRANSCRIPT_COUNT + echo $BQ_VAT_VARIANT_NO_TRANSCRIPT_COUNT + + if [[ $BQ_VAT_ROWS_NO_TRANSCRIPT_COUNT -ne $BQ_VAT_VARIANT_NO_TRANSCRIPT_COUNT ]] + then + echo "The number of rows for variants with no transcripts is incorrect" + echo "Validation has failed" + # exit 1 <-- great! This worked! But need to get by it with my sloppy test data for now! + else + echo "If a vid has a null transcript, then the vid is only in one row of the VAT" + fi + + # ------------------------------------------------ + # VALIDATION #5 + # If a vid has any non-null transcripts then one transcript must be Ensembl (transcript_source) and canonical (is_canonical). + echo "VALIDATION #5" + # TODO Rori needs to actually build this in the first place---I think this should currently fail + + + # ------------------------------------------------ + # VALIDATION #6 + # No vid may have a mix of non-null and null transcripts. + echo "VALIDATION #6" + # Get a list of all distinct vids with non-null transcripts + # Get a list of all distinct vids with no transcripts + # Make sure those lists have no intersection + + # bq query --nouse_legacy_sql --project_id="spec-ops-aou" 'SELECT vids_with_transcript_table.vid, vids_no_transcript_table.vid FROM (SELECT DISTINCT vid FROM `~{dataset_name}.~{vat_table}` WHERE transcript IS NULL) AS vids_no_transcript_table inner join (SELECT DISTINCT vid FROM `~{dataset_name}.~{vat_table}` WHERE transcript IS NOT NULL) AS vids_with_transcript_table on vids_with_transcript_table.vid = vids_no_transcript_table.vid' + + # ------------------------------------------------ + # VALIDATION #7 + # No non-nullable fields contain null values. + # Hmmm--- the use of the vat_schema should do that for us + # Could get a count of each where _ is null + # note that the below returns nothing + # BQ_VAT_NULL=$(bq query --nouse_legacy_sql --project_id=~{project_id} 'SELECT vid FROM `~{dataset_name}.~{vat_table}` WHERE vid IS NULL OR contig IS NULL OR position IS NULL OR ref_allele IS NULL OR alt_allele IS NULL OR variant_type IS NULL OR genomic_location IS NULL' + # vid, contig, position, ref_allele, alt_allele, gvs_all_ac, gvs_all_an, gvs_all_af, variant_type, genomic_location + the aou max stuff Lee still has to figure out + + # ------------------------------------------------ + # VALIDATION #8 + # Each key combination is unique. + # bq query --nouse_legacy_sql --project_id=~{project_id} 'SELECT COUNT (*) FROM `~{dataset_name}.~{vat_table}`' + # BQ_VAT_ROW_COUNT=$(bq query --nouse_legacy_sql --project_id=~{project_id} 'SELECT COUNT (*) FROM `~{dataset_name}.~{vat_table}`') + # bq query --nouse_legacy_sql --project_id=~{project_id} 'SELECT COUNT (DISTINCT vid, DISTINCT transcript) FROM `~{dataset_name}.~{vat_table}`' + # BQ_VAT_KEY_COUNT=$(bq query --nouse_legacy_sql --project_id=~{project_id} 'SELECT COUNT (DISTINCT vid, DISTINCT transcript) FROM `~{dataset_name}.~{vat_table}`') + + # if [ $BQ_VAT_ROW_COUNT -ne $BQ_VAT_KEY_COUNT ]; + # then echo "The number of rows and keys is different" + # exit 1 + # else: + # echo "Each key combination is unique" + # fi + + # ------------------------------------------------ + # FURTHER VALIDATION ?!??! + # Do I want to add additional checks that validate the mapping from the annotations json--ie count instances of 'Ensembl' in the annotations json ? >>> # ------------------------------------------------ # Runtime settings: runtime { docker: "openbridge/ob_google-bigquery:latest" - memory: "3 GB" + memory: "1 GB" cpu: "1" disks: "local-disk 100 HDD" } From cd2eb2f14cc6f710ed3ec411678eeba2bd3a0856 Mon Sep 17 00:00:00 2001 From: Kristian Cibulskis Date: Tue, 29 Jun 2021 10:14:46 -0400 Subject: [PATCH 36/73] testing ideas --- .../create_variant_annotation_table.py | 33 ++++++++++++++----- .../variantstore/wdl/extract/requirements.txt | 1 + 2 files changed, 26 insertions(+), 8 deletions(-) diff --git a/scripts/variantstore/wdl/extract/create_variant_annotation_table.py b/scripts/variantstore/wdl/extract/create_variant_annotation_table.py index 000447663ec..c8e8a96eae2 100644 --- a/scripts/variantstore/wdl/extract/create_variant_annotation_table.py +++ b/scripts/variantstore/wdl/extract/create_variant_annotation_table.py @@ -5,6 +5,8 @@ import csv import json +import ijson +import gzip import argparse JOB_IDS = set() @@ -143,13 +145,18 @@ def make_annotated_json_row(row_position, variant_line, transcript_line): # woul def make_annotation_jsons(annotated_json, output_json, output_genes_json): output_file=open(output_json, 'w') output_genes_file=open(output_genes_json, 'w') - json_data = open(annotated_json, 'r') - data = json.load(json_data) - annotated_position_lines = data['positions'] - annotated_gene_lines = data['genes'] # Is there any reason to split up the genes and positions json creation into two helper scripts? - for annotated_json_line in annotated_position_lines: - position=annotated_json_line.get('position') # this is a required field -- do we want validation? - variants=annotated_json_line.get('variants') + #json_data = open(annotated_json, 'r') + + if annotated_json.endswith(".gz"): + json_data = gzip.open(annotated_json, 'rb') + else: + json_data = open(annotated_json, 'rb') + + positions = ijson.items(json_data, 'positions.item', use_float=True) + + for p in positions: + position=p['position'] # this is a required field -- do we want validation? + variants=p['variants'] # row for each variant - transcript # so let's start with each variant for variant in variants: @@ -168,8 +175,18 @@ def make_annotation_jsons(annotated_json, output_json, output_genes_json): output_file.write(back_json) output_file.write("\n") output_file.close() + + # we've already read the whole file once so we have to open it again + # TODO: cleanup closing of file handles + if annotated_json.endswith(".gz"): + json_data = gzip.open(annotated_json, 'rb') + else: + json_data = open(annotated_json, 'rb') + + genes = ijson.items(json_data, 'genes.item', use_float=True) + omim_fieldnames = list(vat_nirvana_omim_dictionary.keys()) - for gene_line in annotated_gene_lines: + for gene_line in genes: if gene_line.get("omim") != None: row = {} row["gene_symbol"] = gene_line.get("name") # TODO throw an error if it's None? We dont care if there's no omim tho, right? right! cuz nothin would be there to add in the join diff --git a/scripts/variantstore/wdl/extract/requirements.txt b/scripts/variantstore/wdl/extract/requirements.txt index 3700b272e24..969f3857400 100644 --- a/scripts/variantstore/wdl/extract/requirements.txt +++ b/scripts/variantstore/wdl/extract/requirements.txt @@ -1 +1,2 @@ google-cloud-bigquery +ijson From 5ced7641641f93df278acab28f0e6986b41f6ed4 Mon Sep 17 00:00:00 2001 From: rori <6863459+RoriCremer@users.noreply.github.com> Date: Tue, 29 Jun 2021 11:59:14 -0400 Subject: [PATCH 37/73] add new python script to dockerfile --- scripts/variantstore/wdl/extract/Dockerfile | 1 + 1 file changed, 1 insertion(+) diff --git a/scripts/variantstore/wdl/extract/Dockerfile b/scripts/variantstore/wdl/extract/Dockerfile index 5abcfcaab9b..9050fbb336a 100644 --- a/scripts/variantstore/wdl/extract/Dockerfile +++ b/scripts/variantstore/wdl/extract/Dockerfile @@ -6,6 +6,7 @@ RUN pip install -r /app/requirements.txt # Add the application source code. ADD create_cohort_extract_data_table.py /app +ADD create_variant_annotation_table.py /app WORKDIR /app ENTRYPOINT ["/bin/bash"] From 4a1e79f019e551830278cb168245c7aa99c6c520 Mon Sep 17 00:00:00 2001 From: rori <6863459+RoriCremer@users.noreply.github.com> Date: Tue, 29 Jun 2021 12:00:04 -0400 Subject: [PATCH 38/73] spit on compressed json files --- .../create_variant_annotation_table.py | 24 +++++++++---------- 1 file changed, 12 insertions(+), 12 deletions(-) diff --git a/scripts/variantstore/wdl/extract/create_variant_annotation_table.py b/scripts/variantstore/wdl/extract/create_variant_annotation_table.py index c8e8a96eae2..4dec21ce3cb 100644 --- a/scripts/variantstore/wdl/extract/create_variant_annotation_table.py +++ b/scripts/variantstore/wdl/extract/create_variant_annotation_table.py @@ -143,9 +143,9 @@ def make_annotated_json_row(row_position, variant_line, transcript_line): # woul return row def make_annotation_jsons(annotated_json, output_json, output_genes_json): - output_file=open(output_json, 'w') - output_genes_file=open(output_genes_json, 'w') - #json_data = open(annotated_json, 'r') + # TODO split this into two methods---positions and genes + output_file=gzip.open(output_json, 'w') + output_genes_file=gzip.open(output_genes_json, 'w') if annotated_json.endswith(".gz"): json_data = gzip.open(annotated_json, 'rb') @@ -164,16 +164,16 @@ def make_annotation_jsons(annotated_json, output_json, output_genes_json): if variant.get("transcripts") == None: # then we make a special row row = make_annotated_json_row(position, variant, None) - back_json=json.dumps(row) - output_file.write(back_json) - output_file.write("\n") + json_str = json.dumps(row) + "\n" + json_bytes = json_str.encode('utf-8') + output_file.write(json_bytes) else: transcript_lines = variant.get("transcripts") for transcript in transcript_lines: row = make_annotated_json_row(position, variant, transcript) - back_json=json.dumps(row) - output_file.write(back_json) - output_file.write("\n") + json_str = json.dumps(row) + "\n" + json_bytes = json_str.encode('utf-8') + output_file.write(json_bytes) output_file.close() # we've already read the whole file once so we have to open it again @@ -198,9 +198,9 @@ def make_annotation_jsons(annotated_json, output_json, output_genes_json): nirvana_omim_fieldname = vat_nirvana_omim_dictionary.get(vat_omim_fieldname) omim_fieldvalue = phenotypes_line.get(nirvana_omim_fieldname) row[vat_omim_fieldname] = omim_fieldvalue - back_json=json.dumps(row) - output_genes_file.write(back_json) - output_genes_file.write("\n") + json_str = json.dumps(row) + "\n" + json_bytes = json_str.encode('utf-8') + output_genes_file.write(json_bytes) output_genes_file.close() if __name__ == '__main__': From 57fc083b2bc30831a8defea2bd767be1791dc012 Mon Sep 17 00:00:00 2001 From: rori <6863459+RoriCremer@users.noreply.github.com> Date: Tue, 29 Jun 2021 16:07:44 -0400 Subject: [PATCH 39/73] add my wdl to dockstore!?!!? --- .dockstore.yml | 10 ++++++++++ 1 file changed, 10 insertions(+) diff --git a/.dockstore.yml b/.dockstore.yml index 69e65db0482..1c4cd207100 100644 --- a/.dockstore.yml +++ b/.dockstore.yml @@ -89,6 +89,16 @@ workflows: primaryDescriptorPath: /scripts/variantstore/wdl/GvsPrepareCallset.wdl testParameterFiles: - /scripts/variantstore/wdl/GvsPrepareCallset.example.inputs.json + filters: + branches: + - master + - ah_var_store + - rc-318-sites-only-filtered-vcf-then-annotate-wdl + - name: GvsSitesOnlyVCF + subclass: WDL + primaryDescriptorPath: /scripts/variantstore/wdl/GvsSitesOnlyVCF.wdl + testParameterFiles: + - /scripts/variantstore/wdl/GvsSitesOnlyVCF.example.inputs.json filters: branches: - master From bb5374e08ae6be504716b2c37f2f5a8767f26db9 Mon Sep 17 00:00:00 2001 From: rori <6863459+RoriCremer@users.noreply.github.com> Date: Tue, 29 Jun 2021 22:42:34 -0400 Subject: [PATCH 40/73] take into account multiple phenotypes --- .../create_variant_annotation_table.py | 21 ++++++++++--------- 1 file changed, 11 insertions(+), 10 deletions(-) diff --git a/scripts/variantstore/wdl/extract/create_variant_annotation_table.py b/scripts/variantstore/wdl/extract/create_variant_annotation_table.py index 4dec21ce3cb..8a5773b1f6d 100644 --- a/scripts/variantstore/wdl/extract/create_variant_annotation_table.py +++ b/scripts/variantstore/wdl/extract/create_variant_annotation_table.py @@ -38,13 +38,13 @@ "gene_symbol": "hgnc", # nullable "transcript_source": "source", # nullable "aa_change": "hgvsp", # nullable - "consequence": "consequence", # nullable -- TODO check on this one. May want this to be "[]" + "consequence": "consequence", # nullable -- this is now an array "dna_change": "hgvsc", # nullable "exon_number": "exons", # nullable "intron_number": "introns", # nullable - "splice_distance": "hgvsc", # nullable -- TODO Additional processing: Extract the splice distance from the hgvsc field + # "splice_distance": "hgvsc", # nullable -- Lee has pushed this out of p0 for now "entrez_gene_id": "geneId", # nullable - # "hgnc_gene_id": "hgncid", # nullable -- TODO ignore for now Lees notes dont match up here: genes.hgncid? + # "hgnc_gene_id": "hgncid", # nullable -- Lee has pushed this out of p0 for now "is_canonical_transcript": "isCanonical" # nullable -- (and lets make the nulls false) } @@ -86,10 +86,10 @@ } vat_nirvana_omim_dictionary = { # TODO or should this be vat_nirvana_genes_dictionary ? - #"hgnc_gene_id": "hgncid", # nullable genes.hgncid NOT HERE?!??!? + # "hgnc_gene_id": "hgncid", # nullable genes.hgncid NOT HERE -- Lee has pushed this out of p0 for now # "gene_omim_id": "mimNumber", # nullable genes.omim.mimNumber HARD CODED FOR NOW "omim_phenotypes_id": "mimNumber", # nullable <-- lets talk arrays! genes.omim.phenotypes.mimNumber - "omim_phenotypes_name": "phenotype" #TODO where is the omim stuff?????? <-- lets talk arrays! genes.omim.phenotypes.phenotype + "omim_phenotypes_name": "phenotype" # nullable } def make_annotated_json_row(row_position, variant_line, transcript_line): # would it be better to not pass the transcript_line since its dupe data? @@ -193,11 +193,12 @@ def make_annotation_jsons(annotated_json, output_json, output_genes_json): omim_line = gene_line["omim"][0] # TODO I am making the huge assumption that we are only grabbing 1 row["gene_omim_id"] = omim_line.get("mimNumber") if omim_line.get("phenotypes") != None: - phenotypes_line = omim_line["phenotypes"][0] # TODO I am making the huge assumption that we are only grabbing 1 - for vat_omim_fieldname in omim_fieldnames: # like "mimNumber", "phenotype" - nirvana_omim_fieldname = vat_nirvana_omim_dictionary.get(vat_omim_fieldname) - omim_fieldvalue = phenotypes_line.get(nirvana_omim_fieldname) - row[vat_omim_fieldname] = omim_fieldvalue + phenotypes = omim_line["phenotypes"] + for phenotype in phenotypes: + for vat_omim_fieldname in omim_fieldnames: # like "mimNumber", "phenotype" + nirvana_omim_fieldname = vat_nirvana_omim_dictionary.get(vat_omim_fieldname) + omim_fieldvalue = phenotype.get(nirvana_omim_fieldname) + row[vat_omim_fieldname] = omim_fieldvalue json_str = json.dumps(row) + "\n" json_bytes = json_str.encode('utf-8') output_genes_file.write(json_bytes) From 660119a7fc2725cbcbf336eb5030f5e7dd31403e Mon Sep 17 00:00:00 2001 From: rori <6863459+RoriCremer@users.noreply.github.com> Date: Wed, 30 Jun 2021 14:07:27 -0400 Subject: [PATCH 41/73] add branch to dockstore --- .dockstore.yml | 4 +--- 1 file changed, 1 insertion(+), 3 deletions(-) diff --git a/.dockstore.yml b/.dockstore.yml index 1c4cd207100..a84fe39dc0a 100644 --- a/.dockstore.yml +++ b/.dockstore.yml @@ -93,7 +93,6 @@ workflows: branches: - master - ah_var_store - - rc-318-sites-only-filtered-vcf-then-annotate-wdl - name: GvsSitesOnlyVCF subclass: WDL primaryDescriptorPath: /scripts/variantstore/wdl/GvsSitesOnlyVCF.wdl @@ -101,8 +100,7 @@ workflows: - /scripts/variantstore/wdl/GvsSitesOnlyVCF.example.inputs.json filters: branches: - - master - - ah_var_store + - rc-318-sites-only-filtered-vcf-then-annotate-wdl - name: MitochondriaPipeline subclass: WDL primaryDescriptorPath: /scripts/mitochondria_m2_wdl/MitochondriaPipeline.wdl From df8bcda51e92a39b064233537739f03e6774397e Mon Sep 17 00:00:00 2001 From: rori <6863459+RoriCremer@users.noreply.github.com> Date: Wed, 30 Jun 2021 14:57:14 -0400 Subject: [PATCH 42/73] update dockstore again --- .dockstore.yml | 1 + 1 file changed, 1 insertion(+) diff --git a/.dockstore.yml b/.dockstore.yml index a84fe39dc0a..62252fba1b5 100644 --- a/.dockstore.yml +++ b/.dockstore.yml @@ -93,6 +93,7 @@ workflows: branches: - master - ah_var_store + - rc-318-sites-only-filtered-vcf-then-annotate-wdl - name: GvsSitesOnlyVCF subclass: WDL primaryDescriptorPath: /scripts/variantstore/wdl/GvsSitesOnlyVCF.wdl From 8e151142d77ac97c225d6b9a83288fc83ec4c10d Mon Sep 17 00:00:00 2001 From: rori <6863459+RoriCremer@users.noreply.github.com> Date: Wed, 30 Jun 2021 15:15:07 -0400 Subject: [PATCH 43/73] cleanup --- .dockstore.yml | 1 - 1 file changed, 1 deletion(-) diff --git a/.dockstore.yml b/.dockstore.yml index 62252fba1b5..a84fe39dc0a 100644 --- a/.dockstore.yml +++ b/.dockstore.yml @@ -93,7 +93,6 @@ workflows: branches: - master - ah_var_store - - rc-318-sites-only-filtered-vcf-then-annotate-wdl - name: GvsSitesOnlyVCF subclass: WDL primaryDescriptorPath: /scripts/variantstore/wdl/GvsSitesOnlyVCF.wdl From f30cc7ef8de1a9425c921054b7c7af6aa17229a6 Mon Sep 17 00:00:00 2001 From: rori <6863459+RoriCremer@users.noreply.github.com> Date: Thu, 1 Jul 2021 11:07:56 -0400 Subject: [PATCH 44/73] more schema updates --- .../wdl/schemas/vat_genes_schema.json | 36 +++++----- .../variantstore/wdl/schemas/vat_schema.json | 70 +++++++++---------- 2 files changed, 50 insertions(+), 56 deletions(-) diff --git a/scripts/variantstore/wdl/schemas/vat_genes_schema.json b/scripts/variantstore/wdl/schemas/vat_genes_schema.json index fba7027d13a..92d53beb7c2 100644 --- a/scripts/variantstore/wdl/schemas/vat_genes_schema.json +++ b/scripts/variantstore/wdl/schemas/vat_genes_schema.json @@ -5,22 +5,22 @@ "type": "String", "mode": "Nullable" }, -{ -"description": "OMIM ID", -"name": "gene_omim_id", -"type": "Integer", -"mode": "Nullable" -}, -{ -"description": "OMIM Disease ID TODO -- this needs to be swapped to Repeated not nullable", -"name": "omim_phenotypes_id", -"type": "Integer", -"mode": "Nullable" -}, -{ -"description": "OMIM Disease Name TODO -- this needs to be swapped to Repeated not nullable and String not Integer?", -"name": "omim_phenotypes_name", -"type": "String", -"mode": "Nullable" -} + { + "description": "OMIM ID", + "name": "gene_omim_id", + "type": "Integer", + "mode": "Nullable" + }, + { + "description": "OMIM Disease ID", + "name": "omim_phenotypes_id", + "type": "Integer", + "mode": "Repeated" + }, + { + "description": "OMIM Disease Name", + "name": "omim_phenotypes_name", + "type": "String", + "mode": "Repeated" + } ] \ No newline at end of file diff --git a/scripts/variantstore/wdl/schemas/vat_schema.json b/scripts/variantstore/wdl/schemas/vat_schema.json index 65789af26f6..34a8fc171f0 100644 --- a/scripts/variantstore/wdl/schemas/vat_schema.json +++ b/scripts/variantstore/wdl/schemas/vat_schema.json @@ -1,35 +1,41 @@ [ { - "description": "Must be positive. Exact position for a SNP and the position before the alteration in an indel", - "name": "position", - "type": "Integer", - "mode": "Required" - }, - { "description": "Variant ID. Unique string for identifying a variant (as produced by NIRVANA based on a spec from Broad Institute)", "name": "vid", "type": "String", "mode": "Required" - }, - { + }, + { + "description": "Transcript ID. Null indicates that this variant does not overlap any transcripts", + "name": "transcript", + "type": "String", + "mode": "Nullable" + }, + { "description": "Contig names match the hg38 reference", "name": "contig", "type": "String", "mode": "Required" - }, - { + }, + { + "description": "Must be positive. Exact position for a SNP and the position before the alteration in an indel", + "name": "position", + "type": "Integer", + "mode": "Required" + }, + { "description": "base(s). This should always be one base for SNPs and insertions. More than one base for deletions", "name": "ref_allele", "type": "String", "mode": "Required" - }, - { + }, + { "description": "base(s). This should always be one base for SNPs and deletions. More than one base for insertions", "name": "alt_allele", "type": "String", "mode": "Required" - }, - { + }, + { "description": "DNA change type (HGVS)", "name": "variant_type", "type": "String", @@ -42,17 +48,11 @@ "mode": "Required" }, { - "description": "rsID TODO check with Lee about why this json thinks its Repeated not nullable", + "description": "rsID", "name": "dbsnp_rsid", "type": "String", "mode": "Repeated" }, - { - "description": "Transcript ID. Null indicates that this variant does not overlap any transcripts", - "name": "transcript", - "type": "String", - "mode": "Nullable" - }, { "description": "Gene symbol. A variant can have more than one associated gene symbol, since about 3% of genes do overlap", "name": "gene_symbol", @@ -72,14 +72,14 @@ "mode": "Nullable" }, { - "description": "Amino acid change type TODO check with Lee about why this json thinks its Repeated not nullable", + "description": "Amino acid change type", "name": "consequence", "type": "String", "mode": "Repeated" }, { - "description": "HGVS c. nomenclature; DNA change", - "name": "dna_change", + "description": "HGVS c. nomenclature; DNA change in transcript space", + "name": "dna_change_in_transcript", "type": "String", "mode": "Nullable" }, @@ -96,14 +96,8 @@ "mode": "Nullable" }, { - "description": "Splice site distance for introns Will be a positive or negative integer", - "name": "splice_distance", - "type": "String", - "mode": "Nullable" - }, - { - "description": "Entrez/NCBI ID", - "name": "entrez_gene_id", + "description": "Gene ID for the transcript", + "name": "gene_id", "type": "String", "mode": "Nullable" }, @@ -198,10 +192,10 @@ "mode": "Nullable" }, { - "description": "ClinVar Disease Name TODO Repeated", + "description": "ClinVar Disease Name", "name": "clinvar_phenotype", "type": "String", - "mode": "Nullable" + "mode": "Repeated" }, { "description": "gnomAD: 'Total' frequency", @@ -252,15 +246,15 @@ "mode": "Nullable" }, { - "description": "OMIM Disease ID TODO -- this needs to be swapped to Repeated not nullable", + "description": "OMIM Disease ID", "name": "omim_phenotypes_id", "type": "Integer", - "mode": "Nullable" + "mode": "Repeated" }, { - "description": "OMIM Disease Name TODO -- this needs to be swapped to Repeated not nullable?", + "description": "OMIM Disease Name", "name": "omim_phenotypes_name", "type": "String", - "mode": "Nullable" + "mode": "Repeated" } ] From 46441e07fa87c95dcadff0e710a191c9360bf0d1 Mon Sep 17 00:00:00 2001 From: rori <6863459+RoriCremer@users.noreply.github.com> Date: Thu, 1 Jul 2021 11:17:52 -0400 Subject: [PATCH 45/73] update python script --- .../create_variant_annotation_table.py | 84 ++++++++++++------- 1 file changed, 55 insertions(+), 29 deletions(-) diff --git a/scripts/variantstore/wdl/extract/create_variant_annotation_table.py b/scripts/variantstore/wdl/extract/create_variant_annotation_table.py index 8a5773b1f6d..ab80db54ba3 100644 --- a/scripts/variantstore/wdl/extract/create_variant_annotation_table.py +++ b/scripts/variantstore/wdl/extract/create_variant_annotation_table.py @@ -43,7 +43,8 @@ "exon_number": "exons", # nullable "intron_number": "introns", # nullable # "splice_distance": "hgvsc", # nullable -- Lee has pushed this out of p0 for now - "entrez_gene_id": "geneId", # nullable + "gene_id": "geneId", # nullable + # "entrez_gene_id": "geneId", # nullable # "hgnc_gene_id": "hgncid", # nullable -- Lee has pushed this out of p0 for now "is_canonical_transcript": "isCanonical" # nullable -- (and lets make the nulls false) } @@ -105,22 +106,23 @@ def make_annotated_json_row(row_position, variant_line, transcript_line): # woul for vat_transcripts_fieldname in vat_nirvana_transcripts_dictionary.keys(): # like "transcript" nirvana_transcripts_fieldname = vat_nirvana_transcripts_dictionary.get(vat_transcripts_fieldname) transcript_fieldvalue = transcript_line.get(nirvana_transcripts_fieldname) - if nirvana_transcripts_fieldname == "isCanonical" and transcript_fieldvalue != True: # oooof this is ugly - transcript_fieldvalue = False row[vat_transcripts_fieldname] = transcript_fieldvalue + if variant_line.get("spliceAI") != None & transcript_line.get("hgnc") != None: + splice_ai_list = variant_line["spliceAI"] + for splice_ai_obj in splice_ai_list: + # get the splice AI value that matches to the transcript_line transcripts.hgnc to "spliceAI.hgnc" + if splice_ai_obj.get("hgnc") == transcript_line["hgnc"]: + for vat_splice_ai_fieldname in vat_nirvana_splice_ai_dictionary.keys(): # like "splice_ai_acceptor_gain_score" + nirvana_splice_ai_fieldname = vat_nirvana_splice_ai_dictionary.get(vat_splice_ai_fieldname) + splice_ai_fieldvalue = splice_ai_obj.get(nirvana_splice_ai_fieldname) + row[vat_splice_ai_fieldname] = splice_ai_fieldvalue + for vat_gvs_alleles_fieldname in vat_nirvana_gvs_alleles_dictionary.keys(): # like "gvs_all_ac" nirvana_gvs_alleles_fieldname = vat_nirvana_gvs_alleles_dictionary.get(vat_gvs_alleles_fieldname) gvs_alleles_fieldvalue = variant_line.get(nirvana_gvs_alleles_fieldname) row[vat_gvs_alleles_fieldname] = gvs_alleles_fieldvalue - if variant_line.get("spliceAI") != None: - splice_ai_line = variant_line["spliceAI"][0] # TODO I am making the huge assumption that we are only grabbing 1 - for vat_splice_ai_fieldname in vat_nirvana_splice_ai_dictionary.keys(): # like "splice_ai_acceptor_gain_score" - nirvana_splice_ai_fieldname = vat_nirvana_splice_ai_dictionary.get(vat_splice_ai_fieldname) - splice_ai_fieldvalue = splice_ai_line.get(nirvana_splice_ai_fieldname) - row[vat_splice_ai_fieldname] = splice_ai_fieldvalue - if variant_line.get("gnomad") != None: for vat_gnomad_fieldname in vat_nirvana_gnomad_dictionary.keys(): # like "gnomad_all_af" nirvana_gnomad_fieldname = vat_nirvana_gnomad_dictionary.get(vat_gnomad_fieldname) @@ -128,24 +130,24 @@ def make_annotated_json_row(row_position, variant_line, transcript_line): # woul row[vat_gnomad_fieldname] = gnomad_fieldvalue if variant_line.get("clinvar") != None: - clinvar_lines = variant_line["clinvar"] # TODO I am making the huge assumption that this is correctly pulling the RCV one + clinvar_lines = variant_line["clinvar"] for clinvar_correct_line in clinvar_lines: # get the clinvar line with the id that starts with RCV - if clinvar_correct_line.get("id")[:2] == "RCV": # TODO, does this need to be 3, am I being a dummy here? - for vat_clinvar_fieldname in vat_nirvana_clinvar_dictionary.keys(): # like "clinvar_classification" - nirvana_clinvar_fieldname = vat_nirvana_clinvar_dictionary.get(vat_clinvar_fieldname) - clinvar_fieldvalue = clinvar_correct_line.get(nirvana_clinvar_fieldname) - row[vat_clinvar_fieldname] = clinvar_fieldvalue + if clinvar_correct_line.get("id")[:3] == "RCV": + row["clinvar_id"] = clinvar_correct_line.get("id") # For easy validation downstream + for vat_clinvar_fieldname in vat_nirvana_clinvar_dictionary.keys(): # like "clinvar_classification" + nirvana_clinvar_fieldname = vat_nirvana_clinvar_dictionary.get(vat_clinvar_fieldname) + clinvar_fieldvalue = clinvar_correct_line.get(nirvana_clinvar_fieldname) + row[vat_clinvar_fieldname] = clinvar_fieldvalue if variant_line.get("revel") != None: row["revel"] = variant_line.get("revel").get("score") return row -def make_annotation_jsons(annotated_json, output_json, output_genes_json): - # TODO split this into two methods---positions and genes + +def make_positions_json(annotated_json, output_json): output_file=gzip.open(output_json, 'w') - output_genes_file=gzip.open(output_genes_json, 'w') if annotated_json.endswith(".gz"): json_data = gzip.open(annotated_json, 'rb') @@ -154,6 +156,10 @@ def make_annotation_jsons(annotated_json, output_json, output_genes_json): positions = ijson.items(json_data, 'positions.item', use_float=True) + #TODO: filter down to Ensembl transcripts only. + # so we can no longer just check if the transcripts exist or not---need to see if they exist and then if they have transcript_source of "Ensembl" + # TODO is it better to do the transcript_source filtering here in the python, or in BQ? MAYBE BQ is cleaner? + for p in positions: position=p['position'] # this is a required field -- do we want validation? variants=p['variants'] @@ -169,15 +175,26 @@ def make_annotation_jsons(annotated_json, output_json, output_genes_json): output_file.write(json_bytes) else: transcript_lines = variant.get("transcripts") - for transcript in transcript_lines: - row = make_annotated_json_row(position, variant, transcript) + # Collect all the transcript sources and check for if they contain Ensembl <-- this might be a good place for optimization + sources = [transcript.get('source') for transcript in transcript_lines] + if "Ensembl" not in sources: + for transcript in transcript_lines: + if transcript.get('source') == "Ensembl": + row = make_annotated_json_row(position, variant, transcript) + json_str = json.dumps(row) + "\n" + json_bytes = json_str.encode('utf-8') + output_file.write(json_bytes) + else: + # if there are transcripts, but they are not Ensembl, we now only want one row in the VAT, not one row per transcript + row = make_annotated_json_row(position, variant, None) json_str = json.dumps(row) + "\n" json_bytes = json_str.encode('utf-8') output_file.write(json_bytes) output_file.close() - # we've already read the whole file once so we have to open it again - # TODO: cleanup closing of file handles +def make_genes_json(annotated_json, output_genes_json): + output_genes_file=gzip.open(output_genes_json, 'w') + if annotated_json.endswith(".gz"): json_data = gzip.open(annotated_json, 'rb') else: @@ -189,21 +206,32 @@ def make_annotation_jsons(annotated_json, output_json, output_genes_json): for gene_line in genes: if gene_line.get("omim") != None: row = {} - row["gene_symbol"] = gene_line.get("name") # TODO throw an error if it's None? We dont care if there's no omim tho, right? right! cuz nothin would be there to add in the join + row["gene_symbol"] = gene_line.get("name") omim_line = gene_line["omim"][0] # TODO I am making the huge assumption that we are only grabbing 1 row["gene_omim_id"] = omim_line.get("mimNumber") if omim_line.get("phenotypes") != None: phenotypes = omim_line["phenotypes"] - for phenotype in phenotypes: - for vat_omim_fieldname in omim_fieldnames: # like "mimNumber", "phenotype" + for vat_omim_fieldname in omim_fieldnames: # like "mimNumber", "phenotype" + # both of these are arrays -- TODO would it be clearer if this was just hard coded? + omim_field_array=[] + for phenotype in phenotypes: nirvana_omim_fieldname = vat_nirvana_omim_dictionary.get(vat_omim_fieldname) omim_fieldvalue = phenotype.get(nirvana_omim_fieldname) - row[vat_omim_fieldname] = omim_fieldvalue + omim_field_array.append(omim_fieldvalue) + row[vat_omim_fieldname] = omim_field_array json_str = json.dumps(row) + "\n" json_bytes = json_str.encode('utf-8') output_genes_file.write(json_bytes) output_genes_file.close() +def make_annotation_jsons(annotated_json, output_json, output_genes_json): + make_positions_json(annotated_json, output_json) + # we've already read the whole file once so we have to open it again + # TODO: cleanup closing of file handles + make_genes_json(annotated_json, output_genes_json) + # TODO: should we be taking on the ".json.gz" to all the file names? + + if __name__ == '__main__': parser = argparse.ArgumentParser(allow_abbrev=False, description='Create BQ load friendly jsons for VAT creation') parser.add_argument('--annotated_json',type=str, help='nirvana created annotation json', required=True) @@ -217,6 +245,4 @@ def make_annotation_jsons(annotated_json, output_json, output_genes_json): args.output_vt_json, args.output_genes_json) -#make_annotation_jsons("ralpha1.json", "aou_alpha1_shard_annotations_bq_load.json", "aou_alpha1_shard_genes_bq_load.json") -# TODO add this to the ah_var_store docker!!! # TODO do I want to gsutil cp up the files into a bucket here? \ No newline at end of file From dddfc85c1f958445877b90da48dcb657b4763dbf Mon Sep 17 00:00:00 2001 From: rori <6863459+RoriCremer@users.noreply.github.com> Date: Thu, 1 Jul 2021 13:37:08 -0400 Subject: [PATCH 46/73] update wdl --- scripts/variantstore/wdl/GvsSitesOnlyVCF.wdl | 246 ++++++++----------- 1 file changed, 104 insertions(+), 142 deletions(-) diff --git a/scripts/variantstore/wdl/GvsSitesOnlyVCF.wdl b/scripts/variantstore/wdl/GvsSitesOnlyVCF.wdl index c287d67e13d..703c66fd688 100644 --- a/scripts/variantstore/wdl/GvsSitesOnlyVCF.wdl +++ b/scripts/variantstore/wdl/GvsSitesOnlyVCF.wdl @@ -1,10 +1,9 @@ version 1.0 -workflow GvsSitesOnlyVCF { # tested with "gs://broad-dsp-spec-ops/scratch/rcremer/Nirvana/Data/anvil_expected.vcf" +workflow GvsSitesOnlyVCF { input { Array[File] gvs_extract_cohort_filtered_vcfs Array[File] gvs_extract_cohort_filtered_vcf_indices String output_sites_only_file_name - String output_merged_file_name String output_annotated_file_name String project_id String dataset_name @@ -12,42 +11,33 @@ workflow GvsSitesOnlyVCF { # tested with "gs://broad-dsp-spec-ops/scratch/rcreme File nirvana_override_json File nirvana_schema_json_file File vat_vt_schema_json_file - File create_vat_jsons_python_script - String genes_vat_schema = "gene_symbol:STRING,gene_omim_id:INTEGER,omim_phenotypes_id:INTEGER,omim_phenotypes_name:INTEGER" + File vat_genes_schema_json_file File? gatk_override } # TODO need to decide where to specify the name of the VAT table now that it is needed in 2 steps: BigQueryLoadJson and BigQuerySmokeTest <-- should these be one step? - #scatter(i in range(length(gvs_extract_cohort_filtered_vcfs)) ) { - scatter(i in range(length(["1"])) ) { - #call SitesOnlyVcf { - # input: - # vcf_bgz_gts = gvs_extract_cohort_filtered_vcfs[i], - # vcf_index = gvs_extract_cohort_filtered_vcf_indices[i], - # output_filename = "${output_sites_only_file_name}_${i}.sites_only.vcf.gz", - #} - - #call AnnotateShardedVCF { - # input: - # input_vcf = SitesOnlyVcf.output_vcf, - # input_vcf_index = SitesOnlyVcf.output_vcf_idx, - # output_annotated_file_name = "${output_annotated_file_name}_${i}", - # nirvana_data_tar = nirvana_data_directory - #} + scatter(i in range(length(gvs_extract_cohort_filtered_vcfs)) ) { + call SitesOnlyVcf { + input: + vcf_bgz_gts = gvs_extract_cohort_filtered_vcfs[i], + vcf_index = gvs_extract_cohort_filtered_vcf_indices[i], + output_filename = "${output_sites_only_file_name}_${i}.sites_only.vcf.gz", + } + + call AnnotateShardedVCF { + input: + input_vcf = SitesOnlyVcf.output_vcf, + input_vcf_index = SitesOnlyVcf.output_vcf_idx, + output_annotated_file_name = "${output_annotated_file_name}_${i}", + nirvana_data_tar = nirvana_data_directory + } call PrepAnnotationJson { input: - # annotation_json = AnnotateShardedVCF.annotation_json, - annotation_json = nirvana_override_json, - python_script = create_vat_jsons_python_script, - output_name = "${i}.json" - } - - call BucketJson { # TODO should this be it's own step? We are just gsutiling - input: - vt_bq_loading_json = PrepAnnotationJson.vat_vt_json, - genes_bq_loading_json = PrepAnnotationJson.vat_genes_json + annotation_json = AnnotateShardedVCF.annotation_json, + output_name = "${i}.json.gz", + output_path = "gs://broad-dsp-spec-ops/scratch/rcremer/Nirvana/output/jun30/" } } @@ -55,17 +45,18 @@ workflow GvsSitesOnlyVCF { # tested with "gs://broad-dsp-spec-ops/scratch/rcreme input: nirvana_schema = nirvana_schema_json_file, vt_schema = vat_vt_schema_json_file, - genes_schema = genes_vat_schema, + genes_schema = vat_genes_schema_json_file, project_id = project_id, - dataset_name = dataset_name + dataset_name = dataset_name, + output_path = "gs://broad-dsp-spec-ops/scratch/rcremer/Nirvana/output/jun30/" } call BigQuerySmokeTest { input: project_id = project_id, dataset_name = dataset_name, - # annotation_json = AnnotateShardedVCF.annotation_json - annotation_json = nirvana_override_json + annotation_jsons = AnnotateShardedVCF.annotation_json + # annotation_json = nirvana_override_json } } @@ -155,64 +146,34 @@ task AnnotateShardedVCF { } } -task PrepAnnotationJsonJQ { - input { - File annotation_json - File python_script - String output_name - } - - String output_vt_json = "vat_vt_bq_load" + output_name - String output_genes_json = "vat_genes_bq_load" + output_name - - command <<< - set -e - - python ~{python_script} \ - --annotated_json ~{annotation_json} \ - --output_vt_json ~{output_vt_json} \ - --output_genes_json ~{output_genes_json} - - >>> - # ------------------------------------------------ - # Runtime settings: - runtime { - docker: "us.gcr.io/broad-dsde-methods/variantstore-export:091920" - memory: "10 GB" - cpu: "2" - disks: "local-disk 100 HDD" - } - # ------------------------------------------------ - # Outputs: - output { - File vat_vt_json="~{output_vt_json}" - File vat_genes_json="~{output_genes_json}" - } -} - task PrepAnnotationJson { input { File annotation_json - File python_script String output_name + String output_path } String output_vt_json = "vat_vt_bq_load" + output_name String output_genes_json = "vat_genes_bq_load" + output_name + String output_vt_gcp_path = output_path + 'vt/' + String output_genes_gcp_path = output_path + 'genes/' command <<< set -e - python ~{python_script} \ + python3 /app/create_variant_annotation_table.py \ --annotated_json ~{annotation_json} \ --output_vt_json ~{output_vt_json} \ --output_genes_json ~{output_genes_json} + gsutil cp ~{output_vt_json} '~{output_vt_gcp_path}' + gsutil cp ~{output_genes_json} '~{output_genes_gcp_path}' + >>> # ------------------------------------------------ # Runtime settings: runtime { - docker: "us.gcr.io/broad-dsde-methods/variantstore-export:091920" + docker: "us.gcr.io/broad-dsde-methods/variantstore:ah_var_store_20200701" memory: "10 GB" cpu: "2" disks: "local-disk 100 HDD" @@ -225,54 +186,25 @@ task PrepAnnotationJson { } } -task BucketJson { - input { - File vt_bq_loading_json - File genes_bq_loading_json - } - - command <<< - set -e - - gsutil cp ~{vt_bq_loading_json} gs://broad-dsp-spec-ops/scratch/rcremer/Nirvana/output/vt/ - gsutil cp ~{genes_bq_loading_json} gs://broad-dsp-spec-ops/scratch/rcremer/Nirvana/output/genes/ - - >>> - # ------------------------------------------------ - # Runtime settings: - runtime { - docker: "google/cloud-sdk:latest" - memory: "1 GB" - cpu: "1" - disks: "local-disk 100 HDD" - } - # ------------------------------------------------ - # Outputs: - output { - Boolean done = true - } -} - task BigQueryLoadJson { input { File nirvana_schema File vt_schema - String genes_schema + File genes_schema String project_id String dataset_name + String output_path } # I am going to want to have two pre-vat tables. A variant table and a genes table. They will be joined together for the vat table # See if we can grab the annotations json directly from the gcp bucket (so pull it in as a string so it wont) - String vat_table = "vat_jun28" - String variant_transcript_table = "vat_vt" - String genes_table = "vat_genes" + String vat_table = "vat_jun30" + String variant_transcript_table = "vat_vt_jun30" + String genes_table = "vat_genes_jun30" + String vt_path = output_path + 'vt/*' + String genes_path = output_path + 'genes/*' - # TODO there needs to be a LOOP somewhere give that there are now many files in GCP that need to be loaded into BQ - - String vt_jsons_path = "gs://broad-dsp-spec-ops/scratch/rcremer/Nirvana/output/vt/*" - String genes_jsons_path = "gs://broad-dsp-spec-ops/scratch/rcremer/Nirvana/output/genes/*" command <<< @@ -281,14 +213,15 @@ task BigQueryLoadJson { set -e - if [ $BQ_SHOW_RC -ne 0 ]; then + if [ $BQ_SHOW_RC -ne 0 ]; then # do we want to delete if it's still there? no shards on this part of the workflow echo "Creating a pre-vat table ~{dataset_name}.~{variant_transcript_table}" bq --location=US mk --project_id=~{project_id} ~{dataset_name}.~{variant_transcript_table} ~{vt_schema} fi echo "Loading data into a pre-vat table ~{dataset_name}.~{variant_transcript_table}" - # bq --location=US load --project_id=~{project_id} --source_format=NEWLINE_DELIMITED_JSON ~{dataset_name}.~{variant_transcript_table} ~{vt_jsons_path} - bq --location=US load --project_id="spec-ops-aou" --source_format=NEWLINE_DELIMITED_JSON "anvil_100_for_testing.vat_vt" gs://broad-dsp-spec-ops/scratch/rcremer/Nirvana/output/vt/* + echo ~{vt_path} + echo ~{genes_path} + # bq --location=US load --project_id=~{project_id} --source_format=NEWLINE_DELIMITED_JSON ~{dataset_name}.~{variant_transcript_table} ~{vt_path} set +e @@ -303,8 +236,7 @@ task BigQueryLoadJson { fi echo "Loading data into a pre-vat table ~{dataset_name}.~{genes_table}" - # bq --location=US load --project_id=~{project_id} --source_format=NEWLINE_DELIMITED_JSON ~{dataset_name}.~{genes_table} ~{genes_jsons_path} - bq --location=US load --project_id=~{project_id} --source_format=NEWLINE_DELIMITED_JSON ~{dataset_name}.~{genes_table} gs://broad-dsp-spec-ops/scratch/rcremer/Nirvana/output/genes/* + # bq --location=US load --project_id=~{project_id} --source_format=NEWLINE_DELIMITED_JSON ~{dataset_name}.~{genes_table} ~{genes_path} # create the final vat table with the correct fields PARTITION_FIELD="position" @@ -330,6 +262,8 @@ task BigQueryLoadJson { echo "And putting data into it" # now run some giant query in BQ to get this all in the right table + + # Array value was given but no 'sep' attribute was provided" bq query --nouse_legacy_sql --destination_table=~{dataset_name}.~{vat_table} --project_id=~{project_id} \ 'SELECT v.vid, @@ -344,16 +278,17 @@ task BigQueryLoadJson { v.gene_symbol, v.transcript_source, v.aa_change, - v.consequence, #ARRAY_TO_STRING(v.consequence, ",") AS consequence, - v.dna_change, + v.consequence, + v.dna_change_in_transcript, v.variant_type, v.exon_number, v.intron_number, v.genomic_location, #v.hgvsc AS splice_distance has not yet been designed v.dbsnp_rsid, #ARRAY_TO_STRING(v.dbsnp_rsid, ",") AS dbsnp_rsid, - v.entrez_gene_id, - #g.hgnc_gene_id is not produced by Nirvana annotations + v.gene_id, + #v.entrez_gene_id, + #g.hgnc_gene_id, g.gene_omim_id, CASE WHEN ( v.transcript is not null and v.is_canonical_transcript is not True) THEN False WHEN ( v.transcript is not null and v.is_canonical_transcript is True) THEN True END AS is_canonical_transcript, @@ -381,8 +316,9 @@ task BigQueryLoadJson { v.clinvar_phenotype, FROM `~{dataset_name}.~{variant_transcript_table}` as v left join `~{dataset_name}.~{genes_table}` as g on v.gene_symbol = g.gene_symbol' + # the genes table may need to be a distinct * or something to avoid the duplicates that get created from genes that span shards - # TODO why do I sometimes hit an error above, but still make it to the smoke test? + # TODO why do I sometimes hit an error above, but still make it to the smoke test?!?!??! >>> # ------------------------------------------------ # Runtime settings: @@ -403,49 +339,70 @@ task BigQuerySmokeTest { input { String project_id String dataset_name - File annotation_json + Array[File] annotation_jsons } # What I want to do here is query the final table for my expected results # This will be hardcoded for now, but in the future I may want to pull a line out of the annotations json and use thats - String vat_table = "vat_jun26" # TODO seems dangerous to specify this twice + String vat_table = "vat_jun30" # TODO seems dangerous to specify this twice command <<< - set -e + set +e # validate the VAT table - echo "Does this table row look like I expect it to?" # We will pass, or fail, a pipeline run by checking the following + # TODO do we want to bork the pipeline if one of these following rules fail? Or simply collect the errors? + # ------------------------------------------------ # VALIDATION #1 # The number of passing variants in GVS matches the number of variants in the VAT. # TODO this tests the python---what other qs should we ask here? echo "VALIDATION #1" - # Please note that we are counting the number of variants in GVS, not the number of sites, which may add a difficulty to this task. - # TODO should these get broken down more so as not to test my sloppy bash over testing the data? - # TODO should I write this test in python instead?!?!? - # grep -o -i '"vid":' ~{annotation_json} | wc -l - ANNOTATE_JSON_VARIANT_COUNT=$(grep -o -i '"vid":' ~{annotation_json} | wc -l) - echo $ANNOTATE_JSON_VARIANT_COUNT + # The pipeline completed without an error message + # The VAT has data in it + bq query --nouse_legacy_sql --project_id=~{project_id} 'SELECT COUNT (DISTINCT vid) FROM `~{dataset_name}.~{vat_table}`' BQ_VAT_VARIANT_COUNT=$(bq query --nouse_legacy_sql --project_id=~{project_id} 'SELECT COUNT (DISTINCT vid) AS count FROM `~{dataset_name}.~{vat_table}`'| tr -dc '0-9') echo $BQ_VAT_VARIANT_COUNT + if [[ $BQ_VAT_VARIANT_COUNT -le 0 ]] + then + echo "The VAT has no data in it" + echo "Validation has failed" + exit 1 + else + echo "The VAT has been updated" + fi + + # ------------------------------------------------ + # VALIDATION #2 + # The number of passing variants in GVS matches the number of variants in the VAT. + # TODO this tests the python---what other qs should we ask here? + echo "VALIDATION #2" + # Please note that we are counting the number of variants in GVS, not the number of sites, which may add a difficulty to this task. + # TODO should these get broken down more so as not to test my sloppy bash over testing the data? + # TODO should I write this test in python instead?!?!? YES! I think I should!!!! + # grep -o -i '"vid":' ~{sep=" " annotation_jsons} | wc -l + ANNOTATE_JSON_VARIANT_COUNT=$(grep -o -i '"vid":' ~{sep=" " annotation_jsons} | wc -l) + echo $ANNOTATE_JSON_VARIANT_COUNT + + if [[ $ANNOTATE_JSON_VARIANT_COUNT -ne $BQ_VAT_VARIANT_COUNT ]] then echo "The number of variants is incorrect" echo "Validation has failed" - exit 1 + # exit 1 <-- great! This worked! But need to get by it with my sloppy test data for now! else echo "The number of passing variants in GVS matches the number of variants in the VAT" fi # ------------------------------------------------ - # VALIDATION #2 + # VALIDATION #3 # Less than 5% of the variants have a non-null value in the gene field - echo "VALIDATION #2" + # TODO CHECKING WITH LEE --> We dont think 5% is correct + echo "VALIDATION #3" # Get the number of variants which have been joined (TODO is it the actual joining? or just the potential?) bq query --nouse_legacy_sql --project_id=~{project_id} \ 'SELECT COUNT (DISTINCT vid) AS count FROM `~{dataset_name}.~{vat_table}` WHERE gene_symbol IS NOT NULL' @@ -464,9 +421,9 @@ task BigQuerySmokeTest { fi # ------------------------------------------------ - # VALIDATION #3 + # VALIDATION #4 # All variants in the TESK2 gene region (chr1:45,343,883-45,491,163) list multiple genes and those genes are always TESK2 and AL451136.1. - echo "VALIDATION #3" + echo "VALIDATION #4" # TODO ask Lee for help here. I'm not sure how to do this one? # 'SELECT COUNT (DISTINCT vid) AS distinct_vid_count FROM `~{dataset_name}.~{vat_table}` WHERE contig="chr1"' echo "Still need to validate chr1" @@ -474,9 +431,9 @@ task BigQuerySmokeTest { # TODO this is not done! # ------------------------------------------------ - # VALIDATION #4 + # VALIDATION #5 # If a vid has a null transcript, then the vid is only in one row of the VAT. - echo "VALIDATION #4" + echo "VALIDATION #5" # Get a count of all the rows in the vat with no transcript # Get a count of all distinct VID in vat with no transcript # Make sure they are the same @@ -501,16 +458,17 @@ task BigQuerySmokeTest { fi # ------------------------------------------------ - # VALIDATION #5 + # VALIDATION #6 # If a vid has any non-null transcripts then one transcript must be Ensembl (transcript_source) and canonical (is_canonical). - echo "VALIDATION #5" - # TODO Rori needs to actually build this in the first place---I think this should currently fail + echo "VALIDATION #6" + # Lee is removing this for now. + # SELECT vid, string_agg(DISTINCT is_canonical_transcript) as canonical FROM `spec-ops-aou.anvil_100_for_testing.aou_shard_223_vat` where transcript is not null group by vid order by canonical <--there are plenty that are false # ------------------------------------------------ - # VALIDATION #6 + # VALIDATION #7 # No vid may have a mix of non-null and null transcripts. - echo "VALIDATION #6" + echo "VALIDATION #7" # Get a list of all distinct vids with non-null transcripts # Get a list of all distinct vids with no transcripts # Make sure those lists have no intersection @@ -518,8 +476,9 @@ task BigQuerySmokeTest { # bq query --nouse_legacy_sql --project_id="spec-ops-aou" 'SELECT vids_with_transcript_table.vid, vids_no_transcript_table.vid FROM (SELECT DISTINCT vid FROM `~{dataset_name}.~{vat_table}` WHERE transcript IS NULL) AS vids_no_transcript_table inner join (SELECT DISTINCT vid FROM `~{dataset_name}.~{vat_table}` WHERE transcript IS NOT NULL) AS vids_with_transcript_table on vids_with_transcript_table.vid = vids_no_transcript_table.vid' # ------------------------------------------------ - # VALIDATION #7 + # VALIDATION #8 # No non-nullable fields contain null values. + echo "VALIDATION #8" # Hmmm--- the use of the vat_schema should do that for us # Could get a count of each where _ is null # note that the below returns nothing @@ -527,8 +486,9 @@ task BigQuerySmokeTest { # vid, contig, position, ref_allele, alt_allele, gvs_all_ac, gvs_all_an, gvs_all_af, variant_type, genomic_location + the aou max stuff Lee still has to figure out # ------------------------------------------------ - # VALIDATION #8 + # VALIDATION #9 # Each key combination is unique. + echo "VALIDATION #9" # bq query --nouse_legacy_sql --project_id=~{project_id} 'SELECT COUNT (*) FROM `~{dataset_name}.~{vat_table}`' # BQ_VAT_ROW_COUNT=$(bq query --nouse_legacy_sql --project_id=~{project_id} 'SELECT COUNT (*) FROM `~{dataset_name}.~{vat_table}`') # bq query --nouse_legacy_sql --project_id=~{project_id} 'SELECT COUNT (DISTINCT vid, DISTINCT transcript) FROM `~{dataset_name}.~{vat_table}`' @@ -544,6 +504,8 @@ task BigQuerySmokeTest { # ------------------------------------------------ # FURTHER VALIDATION ?!??! # Do I want to add additional checks that validate the mapping from the annotations json--ie count instances of 'Ensembl' in the annotations json ? + # RCA rule in clinvar data? + # check that vt and vat are the same length >>> # ------------------------------------------------ From 9014a1e712f2c6ae5b5365d37023912003ca87ff Mon Sep 17 00:00:00 2001 From: rori <6863459+RoriCremer@users.noreply.github.com> Date: Fri, 2 Jul 2021 19:06:27 -0400 Subject: [PATCH 47/73] add loading data back --- scripts/variantstore/wdl/GvsSitesOnlyVCF.wdl | 53 +++++++++++--------- 1 file changed, 30 insertions(+), 23 deletions(-) diff --git a/scripts/variantstore/wdl/GvsSitesOnlyVCF.wdl b/scripts/variantstore/wdl/GvsSitesOnlyVCF.wdl index 703c66fd688..f5e419fd81d 100644 --- a/scripts/variantstore/wdl/GvsSitesOnlyVCF.wdl +++ b/scripts/variantstore/wdl/GvsSitesOnlyVCF.wdl @@ -8,10 +8,10 @@ workflow GvsSitesOnlyVCF { String project_id String dataset_name File nirvana_data_directory - File nirvana_override_json File nirvana_schema_json_file File vat_vt_schema_json_file File vat_genes_schema_json_file + String output_path # TODO Is there a Path wdl type? File? gatk_override } @@ -37,18 +37,18 @@ workflow GvsSitesOnlyVCF { input: annotation_json = AnnotateShardedVCF.annotation_json, output_name = "${i}.json.gz", - output_path = "gs://broad-dsp-spec-ops/scratch/rcremer/Nirvana/output/jun30/" + output_path = output_path } } - - call BigQueryLoadJson { + # WHY IS THIS GETTING CALLED FIRST!!?!?! (maybe because it thinks we dont need any outputs? Time to add something to pass thru) + call BigQueryLoadJson { # TODO Note that sometimes this seems to be cached even when it hasn't been run with the correct data--prob because nothing seems to have changed input: nirvana_schema = nirvana_schema_json_file, vt_schema = vat_vt_schema_json_file, genes_schema = vat_genes_schema_json_file, project_id = project_id, dataset_name = dataset_name, - output_path = "gs://broad-dsp-spec-ops/scratch/rcremer/Nirvana/output/jun30/" + output_path = output_path } call BigQuerySmokeTest { @@ -56,7 +56,6 @@ workflow GvsSitesOnlyVCF { project_id = project_id, dataset_name = dataset_name, annotation_jsons = AnnotateShardedVCF.annotation_json - # annotation_json = nirvana_override_json } } @@ -157,6 +156,7 @@ task PrepAnnotationJson { String output_genes_json = "vat_genes_bq_load" + output_name String output_vt_gcp_path = output_path + 'vt/' String output_genes_gcp_path = output_path + 'genes/' + String output_ant_gcp_path = output_path + 'annotations/' command <<< set -e @@ -166,6 +166,7 @@ task PrepAnnotationJson { --output_vt_json ~{output_vt_json} \ --output_genes_json ~{output_genes_json} + gsutil cp ~{annotation_json} '~{output_ant_gcp_path}' gsutil cp ~{output_vt_json} '~{output_vt_gcp_path}' gsutil cp ~{output_genes_json} '~{output_genes_gcp_path}' @@ -221,7 +222,7 @@ task BigQueryLoadJson { echo "Loading data into a pre-vat table ~{dataset_name}.~{variant_transcript_table}" echo ~{vt_path} echo ~{genes_path} - # bq --location=US load --project_id=~{project_id} --source_format=NEWLINE_DELIMITED_JSON ~{dataset_name}.~{variant_transcript_table} ~{vt_path} + bq --location=US load --project_id=~{project_id} --source_format=NEWLINE_DELIMITED_JSON ~{dataset_name}.~{variant_transcript_table} ~{vt_path} set +e @@ -236,7 +237,7 @@ task BigQueryLoadJson { fi echo "Loading data into a pre-vat table ~{dataset_name}.~{genes_table}" - # bq --location=US load --project_id=~{project_id} --source_format=NEWLINE_DELIMITED_JSON ~{dataset_name}.~{genes_table} ~{genes_path} + bq --location=US load --project_id=~{project_id} --source_format=NEWLINE_DELIMITED_JSON ~{dataset_name}.~{genes_table} ~{genes_path} # create the final vat table with the correct fields PARTITION_FIELD="position" @@ -318,7 +319,7 @@ task BigQueryLoadJson { left join `~{dataset_name}.~{genes_table}` as g on v.gene_symbol = g.gene_symbol' # the genes table may need to be a distinct * or something to avoid the duplicates that get created from genes that span shards - # TODO why do I sometimes hit an error above, but still make it to the smoke test?!?!??! + # TODO why do I sometimes hit an error above, but still make it to the smoke test?!?!??! Seems like the auth errors dont fail the workflow >>> # ------------------------------------------------ # Runtime settings: @@ -359,6 +360,7 @@ task BigQuerySmokeTest { # VALIDATION #1 # The number of passing variants in GVS matches the number of variants in the VAT. # TODO this tests the python---what other qs should we ask here? + # TODO sometimes when there's an error msg, this is stripping out the #s and doing math with that like a dummy echo "VALIDATION #1" # The pipeline completed without an error message # The VAT has data in it @@ -371,7 +373,7 @@ task BigQuerySmokeTest { then echo "The VAT has no data in it" echo "Validation has failed" - exit 1 + # exit 1 <-- collect the errors? or fail the pipeline? else echo "The VAT has been updated" fi @@ -393,7 +395,7 @@ task BigQuerySmokeTest { then echo "The number of variants is incorrect" echo "Validation has failed" - # exit 1 <-- great! This worked! But need to get by it with my sloppy test data for now! + # exit 1 <-- collect the errors? or fail the pipeline? else echo "The number of passing variants in GVS matches the number of variants in the VAT" fi @@ -415,7 +417,7 @@ task BigQuerySmokeTest { if [[ $PERCENT -gt 5 ]] then echo "There are too many genes" echo "Validation has failed" - # exit 1 <-- great! This worked! But need to get by it with my sloppy test data for now! + # exit 1 <-- collect the errors? or fail the pipeline? else echo "Less than 5% of the variants have a non-null value in the gene field" fi @@ -452,7 +454,7 @@ task BigQuerySmokeTest { then echo "The number of rows for variants with no transcripts is incorrect" echo "Validation has failed" - # exit 1 <-- great! This worked! But need to get by it with my sloppy test data for now! + # exit 1 <-- collect the errors? or fail the pipeline? else echo "If a vid has a null transcript, then the vid is only in one row of the VAT" fi @@ -489,17 +491,22 @@ task BigQuerySmokeTest { # VALIDATION #9 # Each key combination is unique. echo "VALIDATION #9" - # bq query --nouse_legacy_sql --project_id=~{project_id} 'SELECT COUNT (*) FROM `~{dataset_name}.~{vat_table}`' - # BQ_VAT_ROW_COUNT=$(bq query --nouse_legacy_sql --project_id=~{project_id} 'SELECT COUNT (*) FROM `~{dataset_name}.~{vat_table}`') - # bq query --nouse_legacy_sql --project_id=~{project_id} 'SELECT COUNT (DISTINCT vid, DISTINCT transcript) FROM `~{dataset_name}.~{vat_table}`' - # BQ_VAT_KEY_COUNT=$(bq query --nouse_legacy_sql --project_id=~{project_id} 'SELECT COUNT (DISTINCT vid, DISTINCT transcript) FROM `~{dataset_name}.~{vat_table}`') - - # if [ $BQ_VAT_ROW_COUNT -ne $BQ_VAT_KEY_COUNT ]; - # then echo "The number of rows and keys is different" - # exit 1 - # else: - # echo "Each key combination is unique" + # get the sum of all the distinct vids where transcript is null and all the distinct transcript where transcript is not null + BQ_VAT_DISTINCT_VID_NO_TRANSCRIPT=$(bq query --nouse_legacy_sql --project_id=~{project_id} 'SELECT COUNT (DISTINCT vid) FROM `~{dataset_name}.~{vat_table}` WHERE transcript IS NULL') + BQ_VAT_DISTINCT_TRANSCRIPT=$(bq query --nouse_legacy_sql --project_id=~{project_id} 'SELECT COUNT (DISTINCT transcript) FROM `~{dataset_name}.~{vat_table}` WHERE transcript IS NOT NULL') + BQ_VAT_NO_TRANSCRIPT_ROW_COUNT=$(bq query --nouse_legacy_sql --project_id=~{project_id} 'SELECT COUNT (*) FROM `~{dataset_name}.~{vat_table}` WHERE transcript IS NULL') + BQ_VAT_WITH_TRANSCRIPT_ROW_COUNT=$(bq query --nouse_legacy_sql --project_id=~{project_id} 'SELECT COUNT (*) FROM `~{dataset_name}.~{vat_table}` WHERE transcript IS NOT NULL') + + if [ $BQ_VAT_DISTINCT_VID_NO_TRANSCRIPT -ne $BQ_VAT_NO_TRANSCRIPT_ROW_COUNT ]; + then echo "There are duplicate VID rows without transcripts" + # exit 1 <-- collect the errors? or fail the pipeline? # fi + # if [ $BQ_VAT_DISTINCT_TRANSCRIPT -ne $BQ_VAT_WITH_TRANSCRIPT_ROW_COUNT ]; # TODO double check this transcripts bit! + # then echo "The number of rows and keys is different" + # exit 1 <-- collect the errors? or fail the pipeline? + else: + echo "Each key combination is unique" + fi # ------------------------------------------------ # FURTHER VALIDATION ?!??! From d965f3fc7dbe3151680eb31c87e6edcc21f98795 Mon Sep 17 00:00:00 2001 From: rori <6863459+RoriCremer@users.noreply.github.com> Date: Fri, 2 Jul 2021 19:53:10 -0400 Subject: [PATCH 48/73] typo in clinvar_id --- .../create_variant_annotation_table.py | 57 +++++++++++++++---- 1 file changed, 47 insertions(+), 10 deletions(-) diff --git a/scripts/variantstore/wdl/extract/create_variant_annotation_table.py b/scripts/variantstore/wdl/extract/create_variant_annotation_table.py index ab80db54ba3..ba99d9f106c 100644 --- a/scripts/variantstore/wdl/extract/create_variant_annotation_table.py +++ b/scripts/variantstore/wdl/extract/create_variant_annotation_table.py @@ -1,7 +1,7 @@ # -*- coding: utf-8 -*- import uuid import time -import datetime +from datetime import datetime import csv import json @@ -93,6 +93,24 @@ "omim_phenotypes_name": "phenotype" # nullable } +significance_ordering = [ + "Benign", + "Likely Benign", + "Uncertain significance", + "Likely pathogenic", + "Pathogenic", + "drug response", + "association", + "risk factor", + "protective", + "Affects", + "conflicting data from submitters", + "other", + "not provided", + "'-'" + ] + + def make_annotated_json_row(row_position, variant_line, transcript_line): # would it be better to not pass the transcript_line since its dupe data? row = {} row["position"] = row_position # this is a required field -- do we want validation? (what about validation for all the variants_fieldnames?) @@ -131,14 +149,30 @@ def make_annotated_json_row(row_position, variant_line, transcript_line): # woul if variant_line.get("clinvar") != None: clinvar_lines = variant_line["clinvar"] - for clinvar_correct_line in clinvar_lines: - # get the clinvar line with the id that starts with RCV - if clinvar_correct_line.get("id")[:3] == "RCV": - row["clinvar_id"] = clinvar_correct_line.get("id") # For easy validation downstream - for vat_clinvar_fieldname in vat_nirvana_clinvar_dictionary.keys(): # like "clinvar_classification" - nirvana_clinvar_fieldname = vat_nirvana_clinvar_dictionary.get(vat_clinvar_fieldname) - clinvar_fieldvalue = clinvar_correct_line.get(nirvana_clinvar_fieldname) - row[vat_clinvar_fieldname] = clinvar_fieldvalue + significance_values = [] # ordered by Benign, Likely Benign, Uncertain significance, Likely pathogenic, Pathogenic # https://www.ncbi.nlm.nih.gov/clinvar/docs/clinsig/ + updated_dates = [] # grab the most recent + phenotypes = [] # ordered alphabetically + clinvar_ids = [] # For easy validation downstream + for clinvar_RCV_line in clinvar_lines: + # get the clinvar lines with the id that starts with RCV + if clinvar_RCV_line.get("id")[:3] == "RCV": + clinvar_ids.append(clinvar_RCV_line.get("id")) + significance_values.extend(clinvar_RCV_line.get("significance")) + updated_dates.append(clinvar_RCV_line.get("lastUpdatedDate")) + phenotypes.extend(clinvar_RCV_line.get("phenotypes")) + # We want to collect all the significance values and order them by the significance_ordering list + # So I will loop through the significance_ordering values and check for matching values in the significance_values list and put them in a new list + ordered_significance_values = [] + for value in significance_ordering: + if value in significance_values: + ordered_significance_values.append(value) # this adds the id to the end of the list + values_not_accounted_for = list(set(ordered_significance_values).difference(significance_values)) + ordered_significance_values.extend(values_not_accounted_for) # add any values that aren't in significance_ordering to the end + row["clinvar_id"] = clinvar_ids # array + row["clinvar_classification"] = ordered_significance_values # special sorted array + updated_dates.sort(key=lambda date: datetime.strptime(date, "%Y-%m-%d")) # note: method is in-place, and returns None + row["clinvar_last_updated"] = updated_dates[-1] # most recent date + row["clinvar_phenotype"] = sorted(phenotypes) # union of all phenotypes if variant_line.get("revel") != None: row["revel"] = variant_line.get("revel").get("score") @@ -208,6 +242,9 @@ def make_genes_json(annotated_json, output_genes_json): row = {} row["gene_symbol"] = gene_line.get("name") omim_line = gene_line["omim"][0] # TODO I am making the huge assumption that we are only grabbing 1 + if len(gene_line.get("omim")) > 1: + print(gene_line.get("name"),len(gene_line.get("omim"))) + raise ValueError("An assumption about the possible count of omim values is incorrect.") row["gene_omim_id"] = omim_line.get("mimNumber") if omim_line.get("phenotypes") != None: phenotypes = omim_line["phenotypes"] @@ -216,7 +253,7 @@ def make_genes_json(annotated_json, output_genes_json): omim_field_array=[] for phenotype in phenotypes: nirvana_omim_fieldname = vat_nirvana_omim_dictionary.get(vat_omim_fieldname) - omim_fieldvalue = phenotype.get(nirvana_omim_fieldname) + omim_fieldvalue = phenotype.get(nirvana_omim_fieldname, "") omim_field_array.append(omim_fieldvalue) row[vat_omim_fieldname] = omim_field_array json_str = json.dumps(row) + "\n" From ff4d123e6b55ab944c5f560460c6416c5d14d9bf Mon Sep 17 00:00:00 2001 From: rori <6863459+RoriCremer@users.noreply.github.com> Date: Fri, 2 Jul 2021 19:54:11 -0400 Subject: [PATCH 49/73] add updated docker --- scripts/variantstore/wdl/GvsSitesOnlyVCF.wdl | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/scripts/variantstore/wdl/GvsSitesOnlyVCF.wdl b/scripts/variantstore/wdl/GvsSitesOnlyVCF.wdl index f5e419fd81d..afb53669d26 100644 --- a/scripts/variantstore/wdl/GvsSitesOnlyVCF.wdl +++ b/scripts/variantstore/wdl/GvsSitesOnlyVCF.wdl @@ -174,7 +174,7 @@ task PrepAnnotationJson { # ------------------------------------------------ # Runtime settings: runtime { - docker: "us.gcr.io/broad-dsde-methods/variantstore:ah_var_store_20200701" + docker: "us.gcr.io/broad-dsde-methods/variantstore:ah_var_store_20200703" memory: "10 GB" cpu: "2" disks: "local-disk 100 HDD" From d8a802097ab24b6d25d2476e32ce7861df0d77c2 Mon Sep 17 00:00:00 2001 From: rori <6863459+RoriCremer@users.noreply.github.com> Date: Fri, 2 Jul 2021 20:15:35 -0400 Subject: [PATCH 50/73] add done flags --- scripts/variantstore/wdl/GvsSitesOnlyVCF.wdl | 8 ++++++-- 1 file changed, 6 insertions(+), 2 deletions(-) diff --git a/scripts/variantstore/wdl/GvsSitesOnlyVCF.wdl b/scripts/variantstore/wdl/GvsSitesOnlyVCF.wdl index afb53669d26..67bf15ee3a2 100644 --- a/scripts/variantstore/wdl/GvsSitesOnlyVCF.wdl +++ b/scripts/variantstore/wdl/GvsSitesOnlyVCF.wdl @@ -48,7 +48,8 @@ workflow GvsSitesOnlyVCF { genes_schema = vat_genes_schema_json_file, project_id = project_id, dataset_name = dataset_name, - output_path = output_path + output_path = output_path, + prep_jsons_done = PrepAnnotationJson.done } call BigQuerySmokeTest { @@ -56,6 +57,7 @@ workflow GvsSitesOnlyVCF { project_id = project_id, dataset_name = dataset_name, annotation_jsons = AnnotateShardedVCF.annotation_json + load_jsons_done = BigQueryLoadJson.done } } @@ -166,7 +168,6 @@ task PrepAnnotationJson { --output_vt_json ~{output_vt_json} \ --output_genes_json ~{output_genes_json} - gsutil cp ~{annotation_json} '~{output_ant_gcp_path}' gsutil cp ~{output_vt_json} '~{output_vt_gcp_path}' gsutil cp ~{output_genes_json} '~{output_genes_gcp_path}' @@ -184,6 +185,7 @@ task PrepAnnotationJson { output { File vat_vt_json="~{output_vt_json}" File vat_genes_json="~{output_genes_json}" + Boolean done = true } } @@ -195,6 +197,7 @@ task BigQueryLoadJson { String project_id String dataset_name String output_path + Array[String] prep_jsons_done } # I am going to want to have two pre-vat tables. A variant table and a genes table. They will be joined together for the vat table @@ -341,6 +344,7 @@ task BigQuerySmokeTest { String project_id String dataset_name Array[File] annotation_jsons + Boolean load_jsons_done } # What I want to do here is query the final table for my expected results From cdedc8a66dd628d34836ead6ba483c2509306995 Mon Sep 17 00:00:00 2001 From: rori <6863459+RoriCremer@users.noreply.github.com> Date: Fri, 2 Jul 2021 20:16:08 -0400 Subject: [PATCH 51/73] update vat schema --- scripts/variantstore/wdl/GvsSitesOnlyVCF.wdl | 2 +- scripts/variantstore/wdl/schemas/vat_schema.json | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/scripts/variantstore/wdl/GvsSitesOnlyVCF.wdl b/scripts/variantstore/wdl/GvsSitesOnlyVCF.wdl index 67bf15ee3a2..45200e47cc2 100644 --- a/scripts/variantstore/wdl/GvsSitesOnlyVCF.wdl +++ b/scripts/variantstore/wdl/GvsSitesOnlyVCF.wdl @@ -56,7 +56,7 @@ workflow GvsSitesOnlyVCF { input: project_id = project_id, dataset_name = dataset_name, - annotation_jsons = AnnotateShardedVCF.annotation_json + annotation_jsons = AnnotateShardedVCF.annotation_json, load_jsons_done = BigQueryLoadJson.done } } diff --git a/scripts/variantstore/wdl/schemas/vat_schema.json b/scripts/variantstore/wdl/schemas/vat_schema.json index 34a8fc171f0..b734e431caf 100644 --- a/scripts/variantstore/wdl/schemas/vat_schema.json +++ b/scripts/variantstore/wdl/schemas/vat_schema.json @@ -183,7 +183,7 @@ "description": "ClinVar Classification", "name": "clinvar_classification", "type": "String", - "mode": "Nullable" + "mode": "Repeated" }, { "description": "ClinVar Classification Date", From 898e7562f676cbc6f39750e38300f46b19916fb9 Mon Sep 17 00:00:00 2001 From: rori <6863459+RoriCremer@users.noreply.github.com> Date: Tue, 6 Jul 2021 12:19:45 -0400 Subject: [PATCH 52/73] eventually this will need to be all defaults --- .../wdl/GvsSitesOnlyVCF.example.inputs.json | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/scripts/variantstore/wdl/GvsSitesOnlyVCF.example.inputs.json b/scripts/variantstore/wdl/GvsSitesOnlyVCF.example.inputs.json index 8f42fefaac1..d111c5cb1f8 100644 --- a/scripts/variantstore/wdl/GvsSitesOnlyVCF.example.inputs.json +++ b/scripts/variantstore/wdl/GvsSitesOnlyVCF.example.inputs.json @@ -1,14 +1,14 @@ { - "GvsSitesOnlyVCF.gvs_extract_cohort_filtered_vcfs": ["gs://fc-secure-daa074a0-884f-4b67-a79b-cb5cd1556c9f/e73809fa-9ef2-4f3b-965c-846eff4b905e/GvsExtractCallset/48c56780-2520-444f-b1b3-83091a74bb08/call-ExtractTask/shard-223/alpha1_1000_223.vcf.gz", "gs://fc-secure-daa074a0-884f-4b67-a79b-cb5cd1556c9f/e73809fa-9ef2-4f3b-965c-846eff4b905e/GvsExtractCallset/48c56780-2520-444f-b1b3-83091a74bb08/call-ExtractTask/shard-0/alpha1_1000_0.vcf.gz"], - "GvsSitesOnlyVCF.gvs_extract_cohort_filtered_vcf_indices": ["gs://fc-secure-daa074a0-884f-4b67-a79b-cb5cd1556c9f/e73809fa-9ef2-4f3b-965c-846eff4b905e/GvsExtractCallset/48c56780-2520-444f-b1b3-83091a74bb08/call-ExtractTask/shard-223/alpha1_1000_223.vcf.gz.tbi", "gs://fc-secure-daa074a0-884f-4b67-a79b-cb5cd1556c9f/e73809fa-9ef2-4f3b-965c-846eff4b905e/GvsExtractCallset/48c56780-2520-444f-b1b3-83091a74bb08/call-ExtractTask/shard-0/alpha1_1000_0.vcf.gz.tbi"], + "GvsSitesOnlyVCF.gvs_extract_cohort_filtered_vcfs": ["gs://broad-dsp-spec-ops/kcibul/ft/gvs.chr20.vcf.gz", "gs://broad-dsp-spec-ops/scratch/rcremer/Nirvana/Data/gvs_features_0.vcf.gz"], + "GvsSitesOnlyVCF.gvs_extract_cohort_filtered_vcf_indices": ["gs://broad-dsp-spec-ops/kcibul/ft/gvs.chr20.vcf.gz.tbi", "gs://broad-dsp-spec-ops/scratch/rcremer/Nirvana/Data/gvs_features_0.vcf.gz.tbi"], "GvsSitesOnlyVCF.output_sites_only_file_name": "hello_did_I_sites_only", - "GvsSitesOnlyVCF.output_merged_file_name": "hello_did_I_merge", "GvsSitesOnlyVCF.output_annotated_file_name": "hello_did_I_annotate", "GvsSitesOnlyVCF.nirvana_data_directory": "gs://broad-dsp-spec-ops/scratch/rcremer/Nirvana/NirvanaData.tar.gz", "GvsSitesOnlyVCF.nirvana_schema_json_file": "gs://broad-dsp-spec-ops/scratch/rcremer/Nirvana/schemas/vat_schema.json", "GvsSitesOnlyVCF.vat_vt_schema_json_file": "gs://broad-dsp-spec-ops/scratch/rcremer/Nirvana/schemas/vt_schema.json", - "GvsSitesOnlyVCF.nirvana_override_json": "gs://broad-dsp-spec-ops/scratch/rcremer/Nirvana/hello_did_I_annotate.json", - "GvsSitesOnlyVCF.create_vat_jsons_python_script": "gs://broad-dsp-spec-ops/scratch/rcremer/Nirvana/create_vat_jsons_python_script.py", + "GvsSitesOnlyVCF.vat_genes_schema_json_file": "gs://broad-dsp-spec-ops/scratch/rcremer/Nirvana/schemas/genes_schema.json", + "GvsSitesOnlyVCF.output_path": "gs://broad-dsp-spec-ops/scratch/rcremer/Nirvana/output/jul6/", + "GvsSitesOnlyVCF.output_prefix": "jul6", "GvsSitesOnlyVCF.project_id": "spec-ops-aou", "GvsSitesOnlyVCF.dataset_name": "anvil_100_for_testing" } From a2b4b98a78a56b8559f752c1f5f158bef6e559a2 Mon Sep 17 00:00:00 2001 From: rori <6863459+RoriCremer@users.noreply.github.com> Date: Tue, 6 Jul 2021 12:20:24 -0400 Subject: [PATCH 53/73] add a table identifier --- scripts/variantstore/wdl/GvsSitesOnlyVCF.wdl | 17 +++++++++-------- 1 file changed, 9 insertions(+), 8 deletions(-) diff --git a/scripts/variantstore/wdl/GvsSitesOnlyVCF.wdl b/scripts/variantstore/wdl/GvsSitesOnlyVCF.wdl index 45200e47cc2..2d496b800c1 100644 --- a/scripts/variantstore/wdl/GvsSitesOnlyVCF.wdl +++ b/scripts/variantstore/wdl/GvsSitesOnlyVCF.wdl @@ -12,6 +12,7 @@ workflow GvsSitesOnlyVCF { File vat_vt_schema_json_file File vat_genes_schema_json_file String output_path # TODO Is there a Path wdl type? + String output_prefix File? gatk_override } @@ -197,15 +198,16 @@ task BigQueryLoadJson { String project_id String dataset_name String output_path + String output_prefix Array[String] prep_jsons_done } # I am going to want to have two pre-vat tables. A variant table and a genes table. They will be joined together for the vat table # See if we can grab the annotations json directly from the gcp bucket (so pull it in as a string so it wont) - String vat_table = "vat_jun30" - String variant_transcript_table = "vat_vt_jun30" - String genes_table = "vat_genes_jun30" + String vat_table = "vat_" + output_prefix + String variant_transcript_table = "vat_vt_" + output_prefix + String genes_table = "vat_genes_" + output_prefix String vt_path = output_path + 'vt/*' String genes_path = output_path + 'genes/*' @@ -345,12 +347,13 @@ task BigQuerySmokeTest { String dataset_name Array[File] annotation_jsons Boolean load_jsons_done + String output_prefix } # What I want to do here is query the final table for my expected results # This will be hardcoded for now, but in the future I may want to pull a line out of the annotations json and use thats - String vat_table = "vat_jun30" # TODO seems dangerous to specify this twice + String vat_table = "vat_" + output_prefix command <<< set +e @@ -390,11 +393,9 @@ task BigQuerySmokeTest { # Please note that we are counting the number of variants in GVS, not the number of sites, which may add a difficulty to this task. # TODO should these get broken down more so as not to test my sloppy bash over testing the data? # TODO should I write this test in python instead?!?!? YES! I think I should!!!! - # grep -o -i '"vid":' ~{sep=" " annotation_jsons} | wc -l - ANNOTATE_JSON_VARIANT_COUNT=$(grep -o -i '"vid":' ~{sep=" " annotation_jsons} | wc -l) + ANNOTATE_JSON_VARIANT_COUNT=$(gunzip -dc ~{sep=" " annotation_jsons} | grep -o -i '"vid":' | wc -l) echo $ANNOTATE_JSON_VARIANT_COUNT - if [[ $ANNOTATE_JSON_VARIANT_COUNT -ne $BQ_VAT_VARIANT_COUNT ]] then echo "The number of variants is incorrect" @@ -431,7 +432,7 @@ task BigQuerySmokeTest { # All variants in the TESK2 gene region (chr1:45,343,883-45,491,163) list multiple genes and those genes are always TESK2 and AL451136.1. echo "VALIDATION #4" # TODO ask Lee for help here. I'm not sure how to do this one? - # 'SELECT COUNT (DISTINCT vid) AS distinct_vid_count FROM `~{dataset_name}.~{vat_table}` WHERE contig="chr1"' + # 'SELECT COUNT (DISTINCT vid) AS distinct_vid_count FROM `~{dataset_name}.~{vat_table}` WHERE contig = "chr1" and position >= 45343883 and position <= 45491163' echo "Still need to validate chr1" # TODO this is not done! From dc64fd90b82df4ffab6621e2b7655317a10710d7 Mon Sep 17 00:00:00 2001 From: rori <6863459+RoriCremer@users.noreply.github.com> Date: Tue, 6 Jul 2021 12:20:57 -0400 Subject: [PATCH 54/73] fix python typo --- .../extract/create_variant_annotation_table.py | 18 +++++++++--------- 1 file changed, 9 insertions(+), 9 deletions(-) diff --git a/scripts/variantstore/wdl/extract/create_variant_annotation_table.py b/scripts/variantstore/wdl/extract/create_variant_annotation_table.py index ba99d9f106c..5e2e3633de1 100644 --- a/scripts/variantstore/wdl/extract/create_variant_annotation_table.py +++ b/scripts/variantstore/wdl/extract/create_variant_annotation_table.py @@ -93,17 +93,17 @@ "omim_phenotypes_name": "phenotype" # nullable } -significance_ordering = [ - "Benign", - "Likely Benign", - "Uncertain significance", - "Likely pathogenic", - "Pathogenic", +significance_ordering = [ # TODO I have lowercased this---check that this is okay. Nirvana seems to have diff cases :P + "benign", + "likely benign", + "uncertain significance", + "aikely pathogenic", + "aathogenic", "drug response", "association", "risk factor", "protective", - "Affects", + "affects", "conflicting data from submitters", "other", "not provided", @@ -162,7 +162,7 @@ def make_annotated_json_row(row_position, variant_line, transcript_line): # woul phenotypes.extend(clinvar_RCV_line.get("phenotypes")) # We want to collect all the significance values and order them by the significance_ordering list # So I will loop through the significance_ordering values and check for matching values in the significance_values list and put them in a new list - ordered_significance_values = [] + ordered_significance_values = [] # how do we deal with cases issues? for value in significance_ordering: if value in significance_values: ordered_significance_values.append(value) # this adds the id to the end of the list @@ -211,7 +211,7 @@ def make_positions_json(annotated_json, output_json): transcript_lines = variant.get("transcripts") # Collect all the transcript sources and check for if they contain Ensembl <-- this might be a good place for optimization sources = [transcript.get('source') for transcript in transcript_lines] - if "Ensembl" not in sources: + if "Ensembl" in sources: for transcript in transcript_lines: if transcript.get('source') == "Ensembl": row = make_annotated_json_row(position, variant, transcript) From 73d8e5ed2301a24a41b936de9aee323783684300 Mon Sep 17 00:00:00 2001 From: rori <6863459+RoriCremer@users.noreply.github.com> Date: Tue, 6 Jul 2021 12:21:52 -0400 Subject: [PATCH 55/73] update python docker --- scripts/variantstore/wdl/GvsSitesOnlyVCF.wdl | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/scripts/variantstore/wdl/GvsSitesOnlyVCF.wdl b/scripts/variantstore/wdl/GvsSitesOnlyVCF.wdl index 2d496b800c1..5a05e027555 100644 --- a/scripts/variantstore/wdl/GvsSitesOnlyVCF.wdl +++ b/scripts/variantstore/wdl/GvsSitesOnlyVCF.wdl @@ -176,7 +176,7 @@ task PrepAnnotationJson { # ------------------------------------------------ # Runtime settings: runtime { - docker: "us.gcr.io/broad-dsde-methods/variantstore:ah_var_store_20200703" + docker: "us.gcr.io/broad-dsde-methods/variantstore:ah_var_store_20200705" memory: "10 GB" cpu: "2" disks: "local-disk 100 HDD" From 54f741296f4b992834b36311cd81bf9ed7602ff5 Mon Sep 17 00:00:00 2001 From: rori <6863459+RoriCremer@users.noreply.github.com> Date: Tue, 6 Jul 2021 12:27:37 -0400 Subject: [PATCH 56/73] table id --- .../wdl/GvsSitesOnlyVCF.example.inputs.json | 2 +- scripts/variantstore/wdl/GvsSitesOnlyVCF.wdl | 19 ++++++++++--------- 2 files changed, 11 insertions(+), 10 deletions(-) diff --git a/scripts/variantstore/wdl/GvsSitesOnlyVCF.example.inputs.json b/scripts/variantstore/wdl/GvsSitesOnlyVCF.example.inputs.json index d111c5cb1f8..f24d1e914f6 100644 --- a/scripts/variantstore/wdl/GvsSitesOnlyVCF.example.inputs.json +++ b/scripts/variantstore/wdl/GvsSitesOnlyVCF.example.inputs.json @@ -8,7 +8,7 @@ "GvsSitesOnlyVCF.vat_vt_schema_json_file": "gs://broad-dsp-spec-ops/scratch/rcremer/Nirvana/schemas/vt_schema.json", "GvsSitesOnlyVCF.vat_genes_schema_json_file": "gs://broad-dsp-spec-ops/scratch/rcremer/Nirvana/schemas/genes_schema.json", "GvsSitesOnlyVCF.output_path": "gs://broad-dsp-spec-ops/scratch/rcremer/Nirvana/output/jul6/", - "GvsSitesOnlyVCF.output_prefix": "jul6", + "GvsSitesOnlyVCF.table_id": "jul6", "GvsSitesOnlyVCF.project_id": "spec-ops-aou", "GvsSitesOnlyVCF.dataset_name": "anvil_100_for_testing" } diff --git a/scripts/variantstore/wdl/GvsSitesOnlyVCF.wdl b/scripts/variantstore/wdl/GvsSitesOnlyVCF.wdl index 5a05e027555..b80ea4fe82c 100644 --- a/scripts/variantstore/wdl/GvsSitesOnlyVCF.wdl +++ b/scripts/variantstore/wdl/GvsSitesOnlyVCF.wdl @@ -12,7 +12,7 @@ workflow GvsSitesOnlyVCF { File vat_vt_schema_json_file File vat_genes_schema_json_file String output_path # TODO Is there a Path wdl type? - String output_prefix + String table_id File? gatk_override } @@ -41,8 +41,7 @@ workflow GvsSitesOnlyVCF { output_path = output_path } } - # WHY IS THIS GETTING CALLED FIRST!!?!?! (maybe because it thinks we dont need any outputs? Time to add something to pass thru) - call BigQueryLoadJson { # TODO Note that sometimes this seems to be cached even when it hasn't been run with the correct data--prob because nothing seems to have changed + call BigQueryLoadJson { input: nirvana_schema = nirvana_schema_json_file, vt_schema = vat_vt_schema_json_file, @@ -50,6 +49,7 @@ workflow GvsSitesOnlyVCF { project_id = project_id, dataset_name = dataset_name, output_path = output_path, + table_id = table_id, prep_jsons_done = PrepAnnotationJson.done } @@ -57,6 +57,7 @@ workflow GvsSitesOnlyVCF { input: project_id = project_id, dataset_name = dataset_name, + table_id = table_id, annotation_jsons = AnnotateShardedVCF.annotation_json, load_jsons_done = BigQueryLoadJson.done } @@ -198,16 +199,16 @@ task BigQueryLoadJson { String project_id String dataset_name String output_path - String output_prefix + String table_id Array[String] prep_jsons_done } # I am going to want to have two pre-vat tables. A variant table and a genes table. They will be joined together for the vat table # See if we can grab the annotations json directly from the gcp bucket (so pull it in as a string so it wont) - String vat_table = "vat_" + output_prefix - String variant_transcript_table = "vat_vt_" + output_prefix - String genes_table = "vat_genes_" + output_prefix + String vat_table = "vat_" + table_id + String variant_transcript_table = "vat_vt_" + table_id + String genes_table = "vat_genes_" + table_id String vt_path = output_path + 'vt/*' String genes_path = output_path + 'genes/*' @@ -347,13 +348,13 @@ task BigQuerySmokeTest { String dataset_name Array[File] annotation_jsons Boolean load_jsons_done - String output_prefix + String table_id } # What I want to do here is query the final table for my expected results # This will be hardcoded for now, but in the future I may want to pull a line out of the annotations json and use thats - String vat_table = "vat_" + output_prefix + String vat_table = "vat_" + table_id command <<< set +e From 0b2eab43585663ba5f75d9d310379187e8af5b86 Mon Sep 17 00:00:00 2001 From: rori <6863459+RoriCremer@users.noreply.github.com> Date: Tue, 6 Jul 2021 13:12:30 -0400 Subject: [PATCH 57/73] lowercase clinvar --- .../wdl/extract/create_variant_annotation_table.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/scripts/variantstore/wdl/extract/create_variant_annotation_table.py b/scripts/variantstore/wdl/extract/create_variant_annotation_table.py index 5e2e3633de1..f4ce0535aec 100644 --- a/scripts/variantstore/wdl/extract/create_variant_annotation_table.py +++ b/scripts/variantstore/wdl/extract/create_variant_annotation_table.py @@ -126,7 +126,7 @@ def make_annotated_json_row(row_position, variant_line, transcript_line): # woul transcript_fieldvalue = transcript_line.get(nirvana_transcripts_fieldname) row[vat_transcripts_fieldname] = transcript_fieldvalue - if variant_line.get("spliceAI") != None & transcript_line.get("hgnc") != None: + if (test_clinvar.jsonvariant_line.get("spliceAI") != None) and (transcript_line.get("hgnc") != None): splice_ai_list = variant_line["spliceAI"] for splice_ai_obj in splice_ai_list: # get the splice AI value that matches to the transcript_line transcripts.hgnc to "spliceAI.hgnc" @@ -157,7 +157,7 @@ def make_annotated_json_row(row_position, variant_line, transcript_line): # woul # get the clinvar lines with the id that starts with RCV if clinvar_RCV_line.get("id")[:3] == "RCV": clinvar_ids.append(clinvar_RCV_line.get("id")) - significance_values.extend(clinvar_RCV_line.get("significance")) + significance_values.extend([x.lower() for x in clinvar_RCV_line.get("significance")]) updated_dates.append(clinvar_RCV_line.get("lastUpdatedDate")) phenotypes.extend(clinvar_RCV_line.get("phenotypes")) # We want to collect all the significance values and order them by the significance_ordering list From ea8b1e65177c56f25314748049aa9d76d636c7bb Mon Sep 17 00:00:00 2001 From: rori <6863459+RoriCremer@users.noreply.github.com> Date: Tue, 6 Jul 2021 13:13:13 -0400 Subject: [PATCH 58/73] update docker --- scripts/variantstore/wdl/GvsSitesOnlyVCF.wdl | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/scripts/variantstore/wdl/GvsSitesOnlyVCF.wdl b/scripts/variantstore/wdl/GvsSitesOnlyVCF.wdl index b80ea4fe82c..e5153bcb301 100644 --- a/scripts/variantstore/wdl/GvsSitesOnlyVCF.wdl +++ b/scripts/variantstore/wdl/GvsSitesOnlyVCF.wdl @@ -177,7 +177,7 @@ task PrepAnnotationJson { # ------------------------------------------------ # Runtime settings: runtime { - docker: "us.gcr.io/broad-dsde-methods/variantstore:ah_var_store_20200705" + docker: "us.gcr.io/broad-dsde-methods/variantstore:ah_var_store_20200706" memory: "10 GB" cpu: "2" disks: "local-disk 100 HDD" From 01578c367e577dfa50793743755f3a9ae0115ed0 Mon Sep 17 00:00:00 2001 From: rori <6863459+RoriCremer@users.noreply.github.com> Date: Tue, 6 Jul 2021 18:29:15 -0400 Subject: [PATCH 59/73] typo --- .../variantstore/wdl/extract/create_variant_annotation_table.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/scripts/variantstore/wdl/extract/create_variant_annotation_table.py b/scripts/variantstore/wdl/extract/create_variant_annotation_table.py index f4ce0535aec..631a19c094b 100644 --- a/scripts/variantstore/wdl/extract/create_variant_annotation_table.py +++ b/scripts/variantstore/wdl/extract/create_variant_annotation_table.py @@ -126,7 +126,7 @@ def make_annotated_json_row(row_position, variant_line, transcript_line): # woul transcript_fieldvalue = transcript_line.get(nirvana_transcripts_fieldname) row[vat_transcripts_fieldname] = transcript_fieldvalue - if (test_clinvar.jsonvariant_line.get("spliceAI") != None) and (transcript_line.get("hgnc") != None): + if (variant_line.get("spliceAI") != None) and (transcript_line.get("hgnc") != None): splice_ai_list = variant_line["spliceAI"] for splice_ai_obj in splice_ai_list: # get the splice AI value that matches to the transcript_line transcripts.hgnc to "spliceAI.hgnc" From caef68602625024a5ae38ad018a83d65b145316d Mon Sep 17 00:00:00 2001 From: rori <6863459+RoriCremer@users.noreply.github.com> Date: Tue, 6 Jul 2021 18:30:38 -0400 Subject: [PATCH 60/73] update wdl --- scripts/variantstore/wdl/GvsSitesOnlyVCF.wdl | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/scripts/variantstore/wdl/GvsSitesOnlyVCF.wdl b/scripts/variantstore/wdl/GvsSitesOnlyVCF.wdl index e5153bcb301..83a74d47cd1 100644 --- a/scripts/variantstore/wdl/GvsSitesOnlyVCF.wdl +++ b/scripts/variantstore/wdl/GvsSitesOnlyVCF.wdl @@ -177,7 +177,7 @@ task PrepAnnotationJson { # ------------------------------------------------ # Runtime settings: runtime { - docker: "us.gcr.io/broad-dsde-methods/variantstore:ah_var_store_20200706" + docker: "us.gcr.io/broad-dsde-methods/variantstore:ah_var_store_20200707" memory: "10 GB" cpu: "2" disks: "local-disk 100 HDD" From 2bbb8691490658b43ed383d80ff8124a298cbd76 Mon Sep 17 00:00:00 2001 From: rori <6863459+RoriCremer@users.noreply.github.com> Date: Wed, 7 Jul 2021 21:49:02 -0400 Subject: [PATCH 61/73] more validation --- scripts/variantstore/wdl/GvsSitesOnlyVCF.wdl | 93 +++++++++++++++++--- 1 file changed, 81 insertions(+), 12 deletions(-) diff --git a/scripts/variantstore/wdl/GvsSitesOnlyVCF.wdl b/scripts/variantstore/wdl/GvsSitesOnlyVCF.wdl index 83a74d47cd1..eab670cdce6 100644 --- a/scripts/variantstore/wdl/GvsSitesOnlyVCF.wdl +++ b/scripts/variantstore/wdl/GvsSitesOnlyVCF.wdl @@ -26,6 +26,8 @@ workflow GvsSitesOnlyVCF { output_filename = "${output_sites_only_file_name}_${i}.sites_only.vcf.gz", } + # we want a step here that uses bcftools to create a TSV for ac, an and af each and then we will nirvana-ize it and then use it for annotations + call AnnotateShardedVCF { input: input_vcf = SitesOnlyVcf.output_vcf, @@ -96,6 +98,38 @@ task SitesOnlyVcf { } } +task ExtractACANAF { + input { + File vcf_bgz_gts + File vcf_index + String output_filename + } + String output_vcf_idx = basename(output_filename) + ".tbi" # or will this be .idx if from .vcf.gz? or ".tbi" if a .vcf + command <<< + set -e + gatk --java-options "-Xmx2048m" \ + SelectVariants \ + -V ~{vcf_bgz_gts} \ + --exclude-filtered \ + --sites-only-vcf-output \ + -O ~{output_filename} + >>> + # ------------------------------------------------ + # Runtime settings: + runtime { + docker: "broadinstitute/gatk:4.2.0.0" + memory: "3 GB" + cpu: "1" + disks: "local-disk 100 HDD" + } + # ------------------------------------------------ + # Outputs: + output { + File output_vcf="~{output_filename}" + File output_vcf_idx="~{output_vcf_idx}" + } +} + task AnnotateShardedVCF { input { File input_vcf @@ -323,6 +357,7 @@ task BigQueryLoadJson { v.clinvar_phenotype, FROM `~{dataset_name}.~{variant_transcript_table}` as v left join `~{dataset_name}.~{genes_table}` as g on v.gene_symbol = g.gene_symbol' + # (SELECT gene_symbol, ANY_VALUE(gene_omim_id) AS gene_omim_id, ANY_VALUE(omim_phenotypes_id) AS omim_phenotypes_id, ANY_VALUE(omim_phenotypes_name) AS omim_phenotypes_name FROM `~{dataset_name}.~{genes_table}` group by gene_symbol) as g # the genes table may need to be a distinct * or something to avoid the duplicates that get created from genes that span shards # TODO why do I sometimes hit an error above, but still make it to the smoke test?!?!??! Seems like the auth errors dont fail the workflow @@ -384,6 +419,7 @@ task BigQuerySmokeTest { # exit 1 <-- collect the errors? or fail the pipeline? else echo "The VAT has been updated" + echo "Validation #1 has passed" fi # ------------------------------------------------ @@ -404,6 +440,7 @@ task BigQuerySmokeTest { # exit 1 <-- collect the errors? or fail the pipeline? else echo "The number of passing variants in GVS matches the number of variants in the VAT" + echo "Validation #2 has passed" fi # ------------------------------------------------ @@ -426,6 +463,7 @@ task BigQuerySmokeTest { # exit 1 <-- collect the errors? or fail the pipeline? else echo "Less than 5% of the variants have a non-null value in the gene field" + echo "Validation #3 has passed" fi # ------------------------------------------------ @@ -434,9 +472,20 @@ task BigQuerySmokeTest { echo "VALIDATION #4" # TODO ask Lee for help here. I'm not sure how to do this one? # 'SELECT COUNT (DISTINCT vid) AS distinct_vid_count FROM `~{dataset_name}.~{vat_table}` WHERE contig = "chr1" and position >= 45343883 and position <= 45491163' + POSITIONAL_COUNT=$('SELECT COUNT (DISTINCT vid) AS distinct_vid_count FROM `~{dataset_name}.~{vat_table}` WHERE contig = "chr1" and position >= 45343883 and position <= 45491163') + TESK2_COUNT=$('SELECT COUNT (DISTINCT vid) AS distinct_vid_count FROM `~{dataset_name}.~{vat_table}` WHERE contig = "chr1" and position >= 45343883 and position <= 45491163 and gene_symbol="TESK2"') + AL451136_COUNT=$('SELECT COUNT (DISTINCT vid) AS distinct_vid_count FROM `~{dataset_name}.~{vat_table}` WHERE contig = "chr1" and position >= 45343883 and position <= 45491163 and gene_symbol="AL451136.1"') echo "Still need to validate chr1" - # TODO this is not done! + + if [[ $POSITIONAL_COUNT -ne ($TESK2_COUNT + $AL451136_COUNT) ]] + then echo "There are unexpected genes in the TESK2 region" + echo "Validation has failed" + # exit 1 <-- collect the errors? or fail the pipeline? + else + echo "All variants in the TESK2 gene region list multiple genes and those genes are always TESK2 and AL451136.1" + echo "Validation #4 has passed" + fi # ------------------------------------------------ # VALIDATION #5 @@ -463,6 +512,7 @@ task BigQuerySmokeTest { # exit 1 <-- collect the errors? or fail the pipeline? else echo "If a vid has a null transcript, then the vid is only in one row of the VAT" + echo "Validation #5 has passed" fi # ------------------------------------------------ @@ -470,7 +520,20 @@ task BigQuerySmokeTest { # If a vid has any non-null transcripts then one transcript must be Ensembl (transcript_source) and canonical (is_canonical). echo "VALIDATION #6" # Lee is removing this for now. + echo "Lee is removing this for now" # SELECT vid, string_agg(DISTINCT is_canonical_transcript) as canonical FROM `spec-ops-aou.anvil_100_for_testing.aou_shard_223_vat` where transcript is not null group by vid order by canonical <--there are plenty that are false + BQ_VAT_ENSEMBL_COUNT=$(bq query --nouse_legacy_sql --project_id=~{project_id} 'SELECT COUNT(*) AS count FROM `~{dataset_name}.~{vat_table}` where transcript is not null and transcript_source="Ensembl"') + BQ_VAT_TRANSCRIPT_COUNT=$(bq query --nouse_legacy_sql --project_id=~{project_id} 'SELECT COUNT(*) AS count FROM `~{dataset_name}.~{vat_table}` where transcript is not null') + + if [[ $BQ_VAT_ENSEMBL_COUNT -ne $BQ_VAT_TRANSCRIPT_COUNTT ]] + then + echo "All transcripts should be from Ensembl" + echo "Validation has failed" + # exit 1 <-- collect the errors? or fail the pipeline? + else + echo "If a vid has any non-null transcripts then one transcript must be Ensembl" + echo "Validation #6 has passed" + fi # ------------------------------------------------ @@ -490,25 +553,31 @@ task BigQuerySmokeTest { # Hmmm--- the use of the vat_schema should do that for us # Could get a count of each where _ is null # note that the below returns nothing - # BQ_VAT_NULL=$(bq query --nouse_legacy_sql --project_id=~{project_id} 'SELECT vid FROM `~{dataset_name}.~{vat_table}` WHERE vid IS NULL OR contig IS NULL OR position IS NULL OR ref_allele IS NULL OR alt_allele IS NULL OR variant_type IS NULL OR genomic_location IS NULL' + BQ_VAT_NULL=$(bq query --nouse_legacy_sql --project_id=~{project_id} 'SELECT COUNT (DISTINCT vid) as count FROM `~{dataset_name}.~{vat_table}` WHERE vid IS NULL OR contig IS NULL OR position IS NULL OR ref_allele IS NULL OR alt_allele IS NULL OR variant_type IS NULL OR genomic_location IS NULL' # vid, contig, position, ref_allele, alt_allele, gvs_all_ac, gvs_all_an, gvs_all_af, variant_type, genomic_location + the aou max stuff Lee still has to figure out + echo $BQ_VAT_NULL + + if [[ $BQ_VAT_NULL -gt 0 ]] + then echo "A required value is null" + echo "Validation has failed" + # exit 1 <-- collect the errors? or fail the pipeline? + else + echo "No required values are null" + echo "Validation #8 has passed" + fi # ------------------------------------------------ # VALIDATION #9 # Each key combination is unique. echo "VALIDATION #9" # get the sum of all the distinct vids where transcript is null and all the distinct transcript where transcript is not null - BQ_VAT_DISTINCT_VID_NO_TRANSCRIPT=$(bq query --nouse_legacy_sql --project_id=~{project_id} 'SELECT COUNT (DISTINCT vid) FROM `~{dataset_name}.~{vat_table}` WHERE transcript IS NULL') - BQ_VAT_DISTINCT_TRANSCRIPT=$(bq query --nouse_legacy_sql --project_id=~{project_id} 'SELECT COUNT (DISTINCT transcript) FROM `~{dataset_name}.~{vat_table}` WHERE transcript IS NOT NULL') - BQ_VAT_NO_TRANSCRIPT_ROW_COUNT=$(bq query --nouse_legacy_sql --project_id=~{project_id} 'SELECT COUNT (*) FROM `~{dataset_name}.~{vat_table}` WHERE transcript IS NULL') - BQ_VAT_WITH_TRANSCRIPT_ROW_COUNT=$(bq query --nouse_legacy_sql --project_id=~{project_id} 'SELECT COUNT (*) FROM `~{dataset_name}.~{vat_table}` WHERE transcript IS NOT NULL') + BQ_VAT_UNIQUE_IDS_COUNT=$(bq query --nouse_legacy_sql --project_id=~{project_id} 'SELECT COUNT(*) FROM (SELECT vid, transcript FROM `spec-ops-aou.anvil_100_for_testing.vat_jul_6_chr1` group by vid, transcript)') + BQ_VAT_ROW_COUNT=$(bq query --nouse_legacy_sql --project_id=~{project_id} 'SELECT COUNT (*) FROM `~{dataset_name}.~{vat_table}` ') - if [ $BQ_VAT_DISTINCT_VID_NO_TRANSCRIPT -ne $BQ_VAT_NO_TRANSCRIPT_ROW_COUNT ]; - then echo "There are duplicate VID rows without transcripts" - # exit 1 <-- collect the errors? or fail the pipeline? - # fi - # if [ $BQ_VAT_DISTINCT_TRANSCRIPT -ne $BQ_VAT_WITH_TRANSCRIPT_ROW_COUNT ]; # TODO double check this transcripts bit! - # then echo "The number of rows and keys is different" + + if [ $BQ_VAT_UNIQUE_IDS_COUNT -ne $BQ_VAT_ROW_COUNT ]; + then echo "There are duplicate variant - transcript rows" + echo "Validation has failed" # exit 1 <-- collect the errors? or fail the pipeline? else: echo "Each key combination is unique" From efe7267b660789c119cdd19ccb75e00ff232e4b4 Mon Sep 17 00:00:00 2001 From: rori <6863459+RoriCremer@users.noreply.github.com> Date: Wed, 7 Jul 2021 21:49:35 -0400 Subject: [PATCH 62/73] fix python typo --- .../variantstore/wdl/extract/create_variant_annotation_table.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/scripts/variantstore/wdl/extract/create_variant_annotation_table.py b/scripts/variantstore/wdl/extract/create_variant_annotation_table.py index 631a19c094b..c8f1dc31efa 100644 --- a/scripts/variantstore/wdl/extract/create_variant_annotation_table.py +++ b/scripts/variantstore/wdl/extract/create_variant_annotation_table.py @@ -39,7 +39,7 @@ "transcript_source": "source", # nullable "aa_change": "hgvsp", # nullable "consequence": "consequence", # nullable -- this is now an array - "dna_change": "hgvsc", # nullable + "dna_change_in_transcript": "hgvsc", # nullable "exon_number": "exons", # nullable "intron_number": "introns", # nullable # "splice_distance": "hgvsc", # nullable -- Lee has pushed this out of p0 for now From 049d5869b07fe554e71d702f2becce1e939460db Mon Sep 17 00:00:00 2001 From: rori <6863459+RoriCremer@users.noreply.github.com> Date: Thu, 8 Jul 2021 16:10:31 -0400 Subject: [PATCH 63/73] update the query to avoid duplicate genes --- scripts/variantstore/wdl/GvsSitesOnlyVCF.wdl | 28 +++++++++++--------- 1 file changed, 15 insertions(+), 13 deletions(-) diff --git a/scripts/variantstore/wdl/GvsSitesOnlyVCF.wdl b/scripts/variantstore/wdl/GvsSitesOnlyVCF.wdl index eab670cdce6..69c36b6e2ca 100644 --- a/scripts/variantstore/wdl/GvsSitesOnlyVCF.wdl +++ b/scripts/variantstore/wdl/GvsSitesOnlyVCF.wdl @@ -293,6 +293,8 @@ task BigQueryLoadJson { set -e # TODO check the below logic. Seems to be appending.....? + # TODO how do we want to be doing this? With a hash of some sort? + if [ $BQ_SHOW_RC -ne 0 ]; then echo "Creating the vat table ~{dataset_name}.~{vat_table}" bq --location=US mk --project_id=~{project_id} ~{dataset_name}.~{vat_table} ~{nirvana_schema} @@ -302,9 +304,9 @@ task BigQueryLoadJson { fi echo "And putting data into it" - # now run some giant query in BQ to get this all in the right table + # Now we run a giant query in BQ to get this all in the right table and join the genes properly + # Note the genes table join includes the group by to avoid the duplicates that get created from genes that span shards - # Array value was given but no 'sep' attribute was provided" bq query --nouse_legacy_sql --destination_table=~{dataset_name}.~{vat_table} --project_id=~{project_id} \ 'SELECT v.vid, @@ -325,21 +327,21 @@ task BigQueryLoadJson { v.exon_number, v.intron_number, v.genomic_location, - #v.hgvsc AS splice_distance has not yet been designed - v.dbsnp_rsid, #ARRAY_TO_STRING(v.dbsnp_rsid, ",") AS dbsnp_rsid, + # v.hgvsc AS splice_distance + v.dbsnp_rsid, v.gene_id, - #v.entrez_gene_id, - #g.hgnc_gene_id, + # v.entrez_gene_id, + # g.hgnc_gene_id, g.gene_omim_id, CASE WHEN ( v.transcript is not null and v.is_canonical_transcript is not True) THEN False WHEN ( v.transcript is not null and v.is_canonical_transcript is True) THEN True END AS is_canonical_transcript, v.gnomad_all_af, v.gnomad_all_ac, v.gnomad_all_an, - v.gnomad_max_af, # this still needs to be designed - v.gnomad_max_ac, # this still needs to be designed - v.gnomad_max_an, # this still needs to be designed - null AS gnomad_max_subpop, # what is this mapping? + # v.gnomad_max_af, + # v.gnomad_max_ac, + # v.gnomad_max_an, + # null AS gnomad_max_subpop, v.revel, # this is the first value in spliceAI (need to validate that there will only ever be one) v.splice_ai_acceptor_gain_score, @@ -356,9 +358,9 @@ task BigQueryLoadJson { v.clinvar_last_updated, v.clinvar_phenotype, FROM `~{dataset_name}.~{variant_transcript_table}` as v - left join `~{dataset_name}.~{genes_table}` as g on v.gene_symbol = g.gene_symbol' - # (SELECT gene_symbol, ANY_VALUE(gene_omim_id) AS gene_omim_id, ANY_VALUE(omim_phenotypes_id) AS omim_phenotypes_id, ANY_VALUE(omim_phenotypes_name) AS omim_phenotypes_name FROM `~{dataset_name}.~{genes_table}` group by gene_symbol) as g - # the genes table may need to be a distinct * or something to avoid the duplicates that get created from genes that span shards + left join + (SELECT gene_symbol, ANY_VALUE(gene_omim_id) AS gene_omim_id, ANY_VALUE(omim_phenotypes_id) AS omim_phenotypes_id, ANY_VALUE(omim_phenotypes_name) AS omim_phenotypes_name FROM `~{dataset_name}.~{genes_table}` group by gene_symbol) as g + on v.gene_symbol = g.gene_symbol' # TODO why do I sometimes hit an error above, but still make it to the smoke test?!?!??! Seems like the auth errors dont fail the workflow >>> From 4482863e4bc17ead14e82d69810e2ee621c2f212 Mon Sep 17 00:00:00 2001 From: rori <6863459+RoriCremer@users.noreply.github.com> Date: Thu, 8 Jul 2021 16:17:22 -0400 Subject: [PATCH 64/73] clean up validation queries --- scripts/variantstore/wdl/GvsSitesOnlyVCF.wdl | 24 ++++++++++---------- 1 file changed, 12 insertions(+), 12 deletions(-) diff --git a/scripts/variantstore/wdl/GvsSitesOnlyVCF.wdl b/scripts/variantstore/wdl/GvsSitesOnlyVCF.wdl index 69c36b6e2ca..e0b783eb06e 100644 --- a/scripts/variantstore/wdl/GvsSitesOnlyVCF.wdl +++ b/scripts/variantstore/wdl/GvsSitesOnlyVCF.wdl @@ -403,8 +403,6 @@ task BigQuerySmokeTest { # ------------------------------------------------ # VALIDATION #1 - # The number of passing variants in GVS matches the number of variants in the VAT. - # TODO this tests the python---what other qs should we ask here? # TODO sometimes when there's an error msg, this is stripping out the #s and doing math with that like a dummy echo "VALIDATION #1" # The pipeline completed without an error message @@ -454,7 +452,6 @@ task BigQuerySmokeTest { bq query --nouse_legacy_sql --project_id=~{project_id} \ 'SELECT COUNT (DISTINCT vid) AS count FROM `~{dataset_name}.~{vat_table}` WHERE gene_symbol IS NOT NULL' BQ_VAT_GENE_COUNT=$(bq query --nouse_legacy_sql --project_id=~{project_id} 'SELECT COUNT (DISTINCT vid) AS count FROM `~{dataset_name}.~{vat_table}` WHERE gene_symbol IS NOT NULL'| tr -dc '0-9') - echo $BQ_VAT_GENE_COUNT echo "Get the percent" PERCENT=$((BQ_VAT_GENE_COUNT * 100 / BQ_VAT_VARIANT_COUNT)) echo $PERCENT @@ -504,9 +501,6 @@ task BigQuerySmokeTest { 'SELECT COUNT(*) AS count FROM `~{dataset_name}.~{vat_table}` WHERE transcript IS NULL' BQ_VAT_VARIANT_NO_TRANSCRIPT_COUNT=$(bq query --nouse_legacy_sql --project_id=~{project_id} 'SELECT COUNT(*) AS count FROM `~{dataset_name}.~{vat_table}` WHERE transcript IS NULL'| tr -dc '0-9') - echo $BQ_VAT_ROWS_NO_TRANSCRIPT_COUNT - echo $BQ_VAT_VARIANT_NO_TRANSCRIPT_COUNT - if [[ $BQ_VAT_ROWS_NO_TRANSCRIPT_COUNT -ne $BQ_VAT_VARIANT_NO_TRANSCRIPT_COUNT ]] then echo "The number of rows for variants with no transcripts is incorrect" @@ -527,7 +521,7 @@ task BigQuerySmokeTest { BQ_VAT_ENSEMBL_COUNT=$(bq query --nouse_legacy_sql --project_id=~{project_id} 'SELECT COUNT(*) AS count FROM `~{dataset_name}.~{vat_table}` where transcript is not null and transcript_source="Ensembl"') BQ_VAT_TRANSCRIPT_COUNT=$(bq query --nouse_legacy_sql --project_id=~{project_id} 'SELECT COUNT(*) AS count FROM `~{dataset_name}.~{vat_table}` where transcript is not null') - if [[ $BQ_VAT_ENSEMBL_COUNT -ne $BQ_VAT_TRANSCRIPT_COUNTT ]] + if [[ $BQ_VAT_ENSEMBL_COUNT -ne $BQ_VAT_TRANSCRIPT_COUNT ]] then echo "All transcripts should be from Ensembl" echo "Validation has failed" @@ -537,7 +531,6 @@ task BigQuerySmokeTest { echo "Validation #6 has passed" fi - # ------------------------------------------------ # VALIDATION #7 # No vid may have a mix of non-null and null transcripts. @@ -546,7 +539,16 @@ task BigQuerySmokeTest { # Get a list of all distinct vids with no transcripts # Make sure those lists have no intersection - # bq query --nouse_legacy_sql --project_id="spec-ops-aou" 'SELECT vids_with_transcript_table.vid, vids_no_transcript_table.vid FROM (SELECT DISTINCT vid FROM `~{dataset_name}.~{vat_table}` WHERE transcript IS NULL) AS vids_no_transcript_table inner join (SELECT DISTINCT vid FROM `~{dataset_name}.~{vat_table}` WHERE transcript IS NOT NULL) AS vids_with_transcript_table on vids_with_transcript_table.vid = vids_no_transcript_table.vid' + BQ_VAT_VID_OVERLAP=$(bq query --nouse_legacy_sql --project_id="spec-ops-aou" 'SELECT COUNT(vids_with_transcript_table.vid) AS count FROM (SELECT DISTINCT vid FROM `~{dataset_name}.~{vat_table}` WHERE transcript IS NULL) AS vids_no_transcript_table inner join (SELECT DISTINCT vid FROM `~{dataset_name}.~{vat_table}` WHERE transcript IS NOT NULL) AS vids_with_transcript_table on vids_with_transcript_table.vid = vids_no_transcript_table.vid') + + if [[ $BQ_VAT_VID_OVERLAP -gt 0 ]] + then echo "A vid has a mix of non-null and null transcripts" + echo "Validation has failed" + # exit 1 <-- collect the errors? or fail the pipeline? + else + echo "No vids have a mix of non-null and null transcripts" + echo "Validation #7 has passed" + fi # ------------------------------------------------ # VALIDATION #8 @@ -576,13 +578,13 @@ task BigQuerySmokeTest { BQ_VAT_UNIQUE_IDS_COUNT=$(bq query --nouse_legacy_sql --project_id=~{project_id} 'SELECT COUNT(*) FROM (SELECT vid, transcript FROM `spec-ops-aou.anvil_100_for_testing.vat_jul_6_chr1` group by vid, transcript)') BQ_VAT_ROW_COUNT=$(bq query --nouse_legacy_sql --project_id=~{project_id} 'SELECT COUNT (*) FROM `~{dataset_name}.~{vat_table}` ') - if [ $BQ_VAT_UNIQUE_IDS_COUNT -ne $BQ_VAT_ROW_COUNT ]; then echo "There are duplicate variant - transcript rows" echo "Validation has failed" # exit 1 <-- collect the errors? or fail the pipeline? else: echo "Each key combination is unique" + echo "Validation #9 has passed" fi # ------------------------------------------------ @@ -606,5 +608,3 @@ task BigQuerySmokeTest { Boolean done = true } } - - From 0056648ff9810c01670f4e4ec1c535d8b1fb29f3 Mon Sep 17 00:00:00 2001 From: rori <6863459+RoriCremer@users.noreply.github.com> Date: Fri, 9 Jul 2021 12:55:39 -0400 Subject: [PATCH 65/73] update docker image with omim friendly python --- scripts/variantstore/wdl/GvsSitesOnlyVCF.wdl | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/scripts/variantstore/wdl/GvsSitesOnlyVCF.wdl b/scripts/variantstore/wdl/GvsSitesOnlyVCF.wdl index e0b783eb06e..adbb5836d7c 100644 --- a/scripts/variantstore/wdl/GvsSitesOnlyVCF.wdl +++ b/scripts/variantstore/wdl/GvsSitesOnlyVCF.wdl @@ -211,7 +211,7 @@ task PrepAnnotationJson { # ------------------------------------------------ # Runtime settings: runtime { - docker: "us.gcr.io/broad-dsde-methods/variantstore:ah_var_store_20200707" + docker: "us.gcr.io/broad-dsde-methods/variantstore:ah_var_store_20200709" memory: "10 GB" cpu: "2" disks: "local-disk 100 HDD" From 63018ae815c7bed3f021bd2ec96c5bab12fccc31 Mon Sep 17 00:00:00 2001 From: rori <6863459+RoriCremer@users.noreply.github.com> Date: Fri, 9 Jul 2021 12:58:47 -0400 Subject: [PATCH 66/73] remove cols from python that we are pushing to august p0 --- .../wdl/extract/create_variant_annotation_table.py | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/scripts/variantstore/wdl/extract/create_variant_annotation_table.py b/scripts/variantstore/wdl/extract/create_variant_annotation_table.py index c8f1dc31efa..d2f767fc903 100644 --- a/scripts/variantstore/wdl/extract/create_variant_annotation_table.py +++ b/scripts/variantstore/wdl/extract/create_variant_annotation_table.py @@ -80,10 +80,10 @@ "gnomad_all_af": "allAf", # nullable "gnomad_all_ac": "allAc", # nullable "gnomad_all_an": "allAn", # nullable - "gnomad_max_af": "afrAf", # nullable THIS NEEDS MORE THAN JUST A MAPPING - "gnomad_max_ac": "afrAc", # nullable THIS NEEDS MORE THAN JUST A MAPPING - "gnomad_max_an": "afrAn", # nullable THIS NEEDS MORE THAN JUST A MAPPING - "gnomad_max_subpop": "x" #TODO need to choose the correct mapping. Lee says maybe drop for now + # "gnomad_max_af": "afrAf", # nullable THIS NEEDS MORE THAN JUST A MAPPING + # "gnomad_max_ac": "afrAc", # nullable THIS NEEDS MORE THAN JUST A MAPPING + # "gnomad_max_an": "afrAn", # nullable THIS NEEDS MORE THAN JUST A MAPPING + # "gnomad_max_subpop": "x" #TODO need to choose the correct mapping. Lee says maybe drop for now } vat_nirvana_omim_dictionary = { # TODO or should this be vat_nirvana_genes_dictionary ? From c129dcb1e0b3f5d9e52ad9590373b97f130d4b61 Mon Sep 17 00:00:00 2001 From: rori <6863459+RoriCremer@users.noreply.github.com> Date: Fri, 9 Jul 2021 12:59:50 -0400 Subject: [PATCH 67/73] python now omim multi value friendly --- .../wdl/extract/create_variant_annotation_table.py | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/scripts/variantstore/wdl/extract/create_variant_annotation_table.py b/scripts/variantstore/wdl/extract/create_variant_annotation_table.py index d2f767fc903..8cc92401695 100644 --- a/scripts/variantstore/wdl/extract/create_variant_annotation_table.py +++ b/scripts/variantstore/wdl/extract/create_variant_annotation_table.py @@ -243,8 +243,7 @@ def make_genes_json(annotated_json, output_genes_json): row["gene_symbol"] = gene_line.get("name") omim_line = gene_line["omim"][0] # TODO I am making the huge assumption that we are only grabbing 1 if len(gene_line.get("omim")) > 1: - print(gene_line.get("name"),len(gene_line.get("omim"))) - raise ValueError("An assumption about the possible count of omim values is incorrect.") + print("WARNING: An assumption about the possible count of omim values is incorrect.", gene_line.get("name"),len(gene_line.get("omim"))) row["gene_omim_id"] = omim_line.get("mimNumber") if omim_line.get("phenotypes") != None: phenotypes = omim_line["phenotypes"] From eb35986e685a2c2495801b4eb8fedf0a302b222a Mon Sep 17 00:00:00 2001 From: kcibul Date: Sat, 10 Jul 2021 14:21:44 -0400 Subject: [PATCH 68/73] VAT changes for alpha1 (#7345) * private branch * added partial SA support * switch to ssd * update docker * attempt to improve performance and call caching * wip * full SA support * wrong task * added SA to json parsing --- .dockstore.yml | 1 + .../wdl/GvsSitesOnlyVCF.example.inputs.json | 3 +- scripts/variantstore/wdl/GvsSitesOnlyVCF.wdl | 74 +++++++++++++++++-- 3 files changed, 70 insertions(+), 8 deletions(-) diff --git a/.dockstore.yml b/.dockstore.yml index a84fe39dc0a..ad9072e115a 100644 --- a/.dockstore.yml +++ b/.dockstore.yml @@ -101,6 +101,7 @@ workflows: filters: branches: - rc-318-sites-only-filtered-vcf-then-annotate-wdl + - kc_vat - name: MitochondriaPipeline subclass: WDL primaryDescriptorPath: /scripts/mitochondria_m2_wdl/MitochondriaPipeline.wdl diff --git a/scripts/variantstore/wdl/GvsSitesOnlyVCF.example.inputs.json b/scripts/variantstore/wdl/GvsSitesOnlyVCF.example.inputs.json index f24d1e914f6..82da92b9e6b 100644 --- a/scripts/variantstore/wdl/GvsSitesOnlyVCF.example.inputs.json +++ b/scripts/variantstore/wdl/GvsSitesOnlyVCF.example.inputs.json @@ -10,5 +10,6 @@ "GvsSitesOnlyVCF.output_path": "gs://broad-dsp-spec-ops/scratch/rcremer/Nirvana/output/jul6/", "GvsSitesOnlyVCF.table_id": "jul6", "GvsSitesOnlyVCF.project_id": "spec-ops-aou", - "GvsSitesOnlyVCF.dataset_name": "anvil_100_for_testing" + "GvsSitesOnlyVCF.dataset_name": "anvil_100_for_testing", + "GvsSitesOnlyVCF.service_account_json": "gs://fc-secure-e91afe60-ca52-48fa-b4a9-c76fed5a0449/keys/aou_wgs_vumc_prod.json" } diff --git a/scripts/variantstore/wdl/GvsSitesOnlyVCF.wdl b/scripts/variantstore/wdl/GvsSitesOnlyVCF.wdl index adbb5836d7c..3c1bb78f5e5 100644 --- a/scripts/variantstore/wdl/GvsSitesOnlyVCF.wdl +++ b/scripts/variantstore/wdl/GvsSitesOnlyVCF.wdl @@ -13,6 +13,8 @@ workflow GvsSitesOnlyVCF { File vat_genes_schema_json_file String output_path # TODO Is there a Path wdl type? String table_id + + File? service_account_json File? gatk_override } @@ -21,8 +23,9 @@ workflow GvsSitesOnlyVCF { scatter(i in range(length(gvs_extract_cohort_filtered_vcfs)) ) { call SitesOnlyVcf { input: - vcf_bgz_gts = gvs_extract_cohort_filtered_vcfs[i], - vcf_index = gvs_extract_cohort_filtered_vcf_indices[i], + input_vcf = gvs_extract_cohort_filtered_vcfs[i], + input_vcf_index = gvs_extract_cohort_filtered_vcf_indices[i], + service_account_json = service_account_json, output_filename = "${output_sites_only_file_name}_${i}.sites_only.vcf.gz", } @@ -40,7 +43,8 @@ workflow GvsSitesOnlyVCF { input: annotation_json = AnnotateShardedVCF.annotation_json, output_name = "${i}.json.gz", - output_path = output_path + output_path = output_path, + service_account_json = service_account_json, } } call BigQueryLoadJson { @@ -52,6 +56,7 @@ workflow GvsSitesOnlyVCF { dataset_name = dataset_name, output_path = output_path, table_id = table_id, + service_account_json = service_account_json, prep_jsons_done = PrepAnnotationJson.done } @@ -60,6 +65,7 @@ workflow GvsSitesOnlyVCF { project_id = project_id, dataset_name = dataset_name, table_id = table_id, + service_account_json = service_account_json, annotation_jsons = AnnotateShardedVCF.annotation_json, load_jsons_done = BigQueryLoadJson.done } @@ -68,16 +74,43 @@ workflow GvsSitesOnlyVCF { ################################################################################ task SitesOnlyVcf { input { - File vcf_bgz_gts - File vcf_index + File input_vcf + File input_vcf_index + File? service_account_json String output_filename } String output_vcf_idx = basename(output_filename) + ".tbi" # or will this be .idx if from .vcf.gz? or ".tbi" if a .vcf + + String has_service_account_file = if (defined(service_account_json)) then 'true' else 'false' + String input_vcf_basename = basename(input_vcf) + String updated_input_vcf = if (defined(service_account_json)) then input_vcf_basename else input_vcf + + parameter_meta { + input_vcf: { + localization_optional: true + } + input_vcf_index: { + localization_optional: true + } + } command <<< set -e + + if [ ~{has_service_account_file} = 'true' ]; then + export GOOGLE_APPLICATION_CREDENTIALS=~{service_account_json} + gcloud auth activate-service-account --key-file='~{service_account_json}' + + gsutil cp ~{input_vcf} . + gsutil cp ~{input_vcf_index} . + fi + + # Adding `--add-output-vcf-command-line false` so that the VCF header doesn't have a timestamp + # in it so that downstream steps can call cache + gatk --java-options "-Xmx2048m" \ SelectVariants \ - -V ~{vcf_bgz_gts} \ + -V ~{updated_input_vcf} \ + --add-output-vcf-command-line false \ --exclude-filtered \ --sites-only-vcf-output \ -O ~{output_filename} @@ -106,6 +139,7 @@ task ExtractACANAF { } String output_vcf_idx = basename(output_filename) + ".tbi" # or will this be .idx if from .vcf.gz? or ".tbi" if a .vcf command <<< + set -e gatk --java-options "-Xmx2048m" \ SelectVariants \ @@ -173,7 +207,8 @@ task AnnotateShardedVCF { docker: "annotation/nirvana:3.14" # this download is too slow---can we beef this up? memory: "5 GB" cpu: "2" - disks: "local-disk 100 HDD" + preemptible: 5 + disks: "local-disk 250 SSD" } # ------------------------------------------------ # Outputs: @@ -188,6 +223,7 @@ task PrepAnnotationJson { File annotation_json String output_name String output_path + File? service_account_json } String output_vt_json = "vat_vt_bq_load" + output_name @@ -196,6 +232,8 @@ task PrepAnnotationJson { String output_genes_gcp_path = output_path + 'genes/' String output_ant_gcp_path = output_path + 'annotations/' + String has_service_account_file = if (defined(service_account_json)) then 'true' else 'false' + command <<< set -e @@ -204,6 +242,11 @@ task PrepAnnotationJson { --output_vt_json ~{output_vt_json} \ --output_genes_json ~{output_genes_json} + if [ ~{has_service_account_file} = 'true' ]; then + export GOOGLE_APPLICATION_CREDENTIALS=~{service_account_json} + gcloud auth activate-service-account --key-file='~{service_account_json}' + fi + gsutil cp ~{output_vt_json} '~{output_vt_gcp_path}' gsutil cp ~{output_genes_json} '~{output_genes_gcp_path}' @@ -234,6 +277,7 @@ task BigQueryLoadJson { String dataset_name String output_path String table_id + File? service_account_json Array[String] prep_jsons_done } @@ -246,9 +290,16 @@ task BigQueryLoadJson { String vt_path = output_path + 'vt/*' String genes_path = output_path + 'genes/*' + String has_service_account_file = if (defined(service_account_json)) then 'true' else 'false' command <<< + if [ ~{has_service_account_file} = 'true' ]; then + export GOOGLE_APPLICATION_CREDENTIALS=~{service_account_json} + gcloud auth activate-service-account --key-file='~{service_account_json}' + gcloud config set project ~{project_id} + fi + bq show --project_id ~{project_id} ~{dataset_name}.~{variant_transcript_table} > /dev/null BQ_SHOW_RC=$? @@ -385,6 +436,7 @@ task BigQuerySmokeTest { String dataset_name Array[File] annotation_jsons Boolean load_jsons_done + File? service_account_json String table_id } @@ -393,9 +445,17 @@ task BigQuerySmokeTest { String vat_table = "vat_" + table_id + String has_service_account_file = if (defined(service_account_json)) then 'true' else 'false' + command <<< set +e + if [ ~{has_service_account_file} = 'true' ]; then + export GOOGLE_APPLICATION_CREDENTIALS=~{service_account_json} + gcloud auth activate-service-account --key-file='~{service_account_json}' + gcloud config set project ~{project_id} + fi + # validate the VAT table # We will pass, or fail, a pipeline run by checking the following From 816d3634e4774431c41fffc14072850c4653a683 Mon Sep 17 00:00:00 2001 From: rori <6863459+RoriCremer@users.noreply.github.com> Date: Mon, 12 Jul 2021 15:49:12 -0400 Subject: [PATCH 69/73] optimize wdl --- scripts/variantstore/wdl/GvsSitesOnlyVCF.wdl | 37 ++++++++++++-------- 1 file changed, 22 insertions(+), 15 deletions(-) diff --git a/scripts/variantstore/wdl/GvsSitesOnlyVCF.wdl b/scripts/variantstore/wdl/GvsSitesOnlyVCF.wdl index 3c1bb78f5e5..9270204d203 100644 --- a/scripts/variantstore/wdl/GvsSitesOnlyVCF.wdl +++ b/scripts/variantstore/wdl/GvsSitesOnlyVCF.wdl @@ -120,6 +120,7 @@ task SitesOnlyVcf { runtime { docker: "broadinstitute/gatk:4.2.0.0" memory: "3 GB" + preemptible: 3 cpu: "1" disks: "local-disk 100 HDD" } @@ -154,6 +155,7 @@ task ExtractACANAF { docker: "broadinstitute/gatk:4.2.0.0" memory: "3 GB" cpu: "1" + preemptible: 3 disks: "local-disk 100 HDD" } # ------------------------------------------------ @@ -204,7 +206,7 @@ task AnnotateShardedVCF { # ------------------------------------------------ # Runtime settings: runtime { - docker: "annotation/nirvana:3.14" # this download is too slow---can we beef this up? + docker: "annotation/nirvana:3.14" memory: "5 GB" cpu: "2" preemptible: 5 @@ -252,12 +254,13 @@ task PrepAnnotationJson { >>> # ------------------------------------------------ - # Runtime settings: + # Runtime settings: # TODO this would be worth tweaking runtime { docker: "us.gcr.io/broad-dsde-methods/variantstore:ah_var_store_20200709" - memory: "10 GB" - cpu: "2" - disks: "local-disk 100 HDD" + memory: "3 GB" + preemptible: 5 + cpu: "1" + disks: "local-disk 250 SSD" } # ------------------------------------------------ # Outputs: @@ -269,6 +272,10 @@ task PrepAnnotationJson { } task BigQueryLoadJson { + meta { # since the WDL will not see the updated data (its getting put in a gcp bucket) + volatile: true + } + input { File nirvana_schema File vt_schema @@ -420,6 +427,7 @@ task BigQueryLoadJson { runtime { docker: "openbridge/ob_google-bigquery:latest" memory: "3 GB" + preemptible: 3 cpu: "1" disks: "local-disk 100 HDD" } @@ -491,6 +499,9 @@ task BigQuerySmokeTest { # TODO should these get broken down more so as not to test my sloppy bash over testing the data? # TODO should I write this test in python instead?!?!? YES! I think I should!!!! ANNOTATE_JSON_VARIANT_COUNT=$(gunzip -dc ~{sep=" " annotation_jsons} | grep -o -i '"vid":' | wc -l) + + # TODO do we want to also count the number of alleles in the final VCF? <-- might be worth asking Lee to clarify!!!! + echo $ANNOTATE_JSON_VARIANT_COUNT if [[ $ANNOTATE_JSON_VARIANT_COUNT -ne $BQ_VAT_VARIANT_COUNT ]] @@ -508,15 +519,13 @@ task BigQuerySmokeTest { # Less than 5% of the variants have a non-null value in the gene field # TODO CHECKING WITH LEE --> We dont think 5% is correct echo "VALIDATION #3" - # Get the number of variants which have been joined (TODO is it the actual joining? or just the potential?) - bq query --nouse_legacy_sql --project_id=~{project_id} \ - 'SELECT COUNT (DISTINCT vid) AS count FROM `~{dataset_name}.~{vat_table}` WHERE gene_symbol IS NOT NULL' + # Get the number of variants which have been joined BQ_VAT_GENE_COUNT=$(bq query --nouse_legacy_sql --project_id=~{project_id} 'SELECT COUNT (DISTINCT vid) AS count FROM `~{dataset_name}.~{vat_table}` WHERE gene_symbol IS NOT NULL'| tr -dc '0-9') echo "Get the percent" PERCENT=$((BQ_VAT_GENE_COUNT * 100 / BQ_VAT_VARIANT_COUNT)) echo $PERCENT - if [[ $PERCENT -gt 5 ]] + if [[ $PERCENT -gt 25 ]] then echo "There are too many genes" echo "Validation has failed" # exit 1 <-- collect the errors? or fail the pipeline? @@ -535,9 +544,10 @@ task BigQuerySmokeTest { TESK2_COUNT=$('SELECT COUNT (DISTINCT vid) AS distinct_vid_count FROM `~{dataset_name}.~{vat_table}` WHERE contig = "chr1" and position >= 45343883 and position <= 45491163 and gene_symbol="TESK2"') AL451136_COUNT=$('SELECT COUNT (DISTINCT vid) AS distinct_vid_count FROM `~{dataset_name}.~{vat_table}` WHERE contig = "chr1" and position >= 45343883 and position <= 45491163 and gene_symbol="AL451136.1"') echo "Still need to validate chr1" + GENE_COUNT_SUM=$(( $TESK2_COUNT + $AL451136_COUNT )) - if [[ $POSITIONAL_COUNT -ne ($TESK2_COUNT + $AL451136_COUNT) ]] + if [[ $POSITIONAL_COUNT -ne $GENE_COUNT_SUM ]] then echo "There are unexpected genes in the TESK2 region" echo "Validation has failed" # exit 1 <-- collect the errors? or fail the pipeline? @@ -554,11 +564,7 @@ task BigQuerySmokeTest { # Get a count of all distinct VID in vat with no transcript # Make sure they are the same # TODO we could in the future specify which VIDs are not distinct - bq query --nouse_legacy_sql --project_id=~{project_id} \ - 'SELECT COUNT (DISTINCT vid) AS distinct_vid_count FROM `~{dataset_name}.~{vat_table}` WHERE transcript IS NULL' BQ_VAT_ROWS_NO_TRANSCRIPT_COUNT=$(bq query --nouse_legacy_sql --project_id=~{project_id} 'SELECT COUNT (DISTINCT vid) AS distinct_vid_count FROM `~{dataset_name}.~{vat_table}` WHERE transcript IS NULL'| tr -dc '0-9') - bq query --nouse_legacy_sql --project_id=~{project_id} \ - 'SELECT COUNT(*) AS count FROM `~{dataset_name}.~{vat_table}` WHERE transcript IS NULL' BQ_VAT_VARIANT_NO_TRANSCRIPT_COUNT=$(bq query --nouse_legacy_sql --project_id=~{project_id} 'SELECT COUNT(*) AS count FROM `~{dataset_name}.~{vat_table}` WHERE transcript IS NULL'| tr -dc '0-9') if [[ $BQ_VAT_ROWS_NO_TRANSCRIPT_COUNT -ne $BQ_VAT_VARIANT_NO_TRANSCRIPT_COUNT ]] @@ -635,7 +641,7 @@ task BigQuerySmokeTest { # Each key combination is unique. echo "VALIDATION #9" # get the sum of all the distinct vids where transcript is null and all the distinct transcript where transcript is not null - BQ_VAT_UNIQUE_IDS_COUNT=$(bq query --nouse_legacy_sql --project_id=~{project_id} 'SELECT COUNT(*) FROM (SELECT vid, transcript FROM `spec-ops-aou.anvil_100_for_testing.vat_jul_6_chr1` group by vid, transcript)') + BQ_VAT_UNIQUE_IDS_COUNT=$(bq query --nouse_legacy_sql --project_id=~{project_id} 'SELECT COUNT(*) FROM (SELECT vid, transcript FROM `~{dataset_name}.~{vat_table}` group by vid, transcript)') BQ_VAT_ROW_COUNT=$(bq query --nouse_legacy_sql --project_id=~{project_id} 'SELECT COUNT (*) FROM `~{dataset_name}.~{vat_table}` ') if [ $BQ_VAT_UNIQUE_IDS_COUNT -ne $BQ_VAT_ROW_COUNT ]; @@ -659,6 +665,7 @@ task BigQuerySmokeTest { runtime { docker: "openbridge/ob_google-bigquery:latest" memory: "1 GB" + preemptible: 3 cpu: "1" disks: "local-disk 100 HDD" } From 56eaa65d9b3d95ad018412c0bcea008c56fe447a Mon Sep 17 00:00:00 2001 From: rori <6863459+RoriCremer@users.noreply.github.com> Date: Tue, 13 Jul 2021 16:01:11 -0400 Subject: [PATCH 70/73] pr review w bec --- .dockstore.yml | 3 +- scripts/variantstore/wdl/GvsSitesOnlyVCF.wdl | 228 +++++------------- .../create_variant_annotation_table.py | 59 ++--- 3 files changed, 80 insertions(+), 210 deletions(-) diff --git a/.dockstore.yml b/.dockstore.yml index ad9072e115a..51a6443144f 100644 --- a/.dockstore.yml +++ b/.dockstore.yml @@ -100,8 +100,7 @@ workflows: - /scripts/variantstore/wdl/GvsSitesOnlyVCF.example.inputs.json filters: branches: - - rc-318-sites-only-filtered-vcf-then-annotate-wdl - - kc_vat + - ah_var_store - name: MitochondriaPipeline subclass: WDL primaryDescriptorPath: /scripts/mitochondria_m2_wdl/MitochondriaPipeline.wdl diff --git a/scripts/variantstore/wdl/GvsSitesOnlyVCF.wdl b/scripts/variantstore/wdl/GvsSitesOnlyVCF.wdl index 9270204d203..53848b547d1 100644 --- a/scripts/variantstore/wdl/GvsSitesOnlyVCF.wdl +++ b/scripts/variantstore/wdl/GvsSitesOnlyVCF.wdl @@ -11,15 +11,13 @@ workflow GvsSitesOnlyVCF { File nirvana_schema_json_file File vat_vt_schema_json_file File vat_genes_schema_json_file - String output_path # TODO Is there a Path wdl type? - String table_id + String output_path + String table_suffix File? service_account_json File? gatk_override } - # TODO need to decide where to specify the name of the VAT table now that it is needed in 2 steps: BigQueryLoadJson and BigQuerySmokeTest <-- should these be one step? - scatter(i in range(length(gvs_extract_cohort_filtered_vcfs)) ) { call SitesOnlyVcf { input: @@ -29,8 +27,6 @@ workflow GvsSitesOnlyVCF { output_filename = "${output_sites_only_file_name}_${i}.sites_only.vcf.gz", } - # we want a step here that uses bcftools to create a TSV for ac, an and af each and then we will nirvana-ize it and then use it for annotations - call AnnotateShardedVCF { input: input_vcf = SitesOnlyVcf.output_vcf, @@ -55,7 +51,7 @@ workflow GvsSitesOnlyVCF { project_id = project_id, dataset_name = dataset_name, output_path = output_path, - table_id = table_id, + table_suffix = table_suffix, service_account_json = service_account_json, prep_jsons_done = PrepAnnotationJson.done } @@ -64,7 +60,7 @@ workflow GvsSitesOnlyVCF { input: project_id = project_id, dataset_name = dataset_name, - table_id = table_id, + table_suffix = table_suffix, service_account_json = service_account_json, annotation_jsons = AnnotateShardedVCF.annotation_json, load_jsons_done = BigQueryLoadJson.done @@ -79,7 +75,7 @@ task SitesOnlyVcf { File? service_account_json String output_filename } - String output_vcf_idx = basename(output_filename) + ".tbi" # or will this be .idx if from .vcf.gz? or ".tbi" if a .vcf + String output_vcf_idx = basename(output_filename) + ".tbi" String has_service_account_file = if (defined(service_account_json)) then 'true' else 'false' String input_vcf_basename = basename(input_vcf) @@ -132,40 +128,6 @@ task SitesOnlyVcf { } } -task ExtractACANAF { - input { - File vcf_bgz_gts - File vcf_index - String output_filename - } - String output_vcf_idx = basename(output_filename) + ".tbi" # or will this be .idx if from .vcf.gz? or ".tbi" if a .vcf - command <<< - - set -e - gatk --java-options "-Xmx2048m" \ - SelectVariants \ - -V ~{vcf_bgz_gts} \ - --exclude-filtered \ - --sites-only-vcf-output \ - -O ~{output_filename} - >>> - # ------------------------------------------------ - # Runtime settings: - runtime { - docker: "broadinstitute/gatk:4.2.0.0" - memory: "3 GB" - cpu: "1" - preemptible: 3 - disks: "local-disk 100 HDD" - } - # ------------------------------------------------ - # Outputs: - output { - File output_vcf="~{output_filename}" - File output_vcf_idx="~{output_vcf_idx}" - } -} - task AnnotateShardedVCF { input { File input_vcf @@ -254,7 +216,7 @@ task PrepAnnotationJson { >>> # ------------------------------------------------ - # Runtime settings: # TODO this would be worth tweaking + # Runtime settings: runtime { docker: "us.gcr.io/broad-dsde-methods/variantstore:ah_var_store_20200709" memory: "3 GB" @@ -283,17 +245,16 @@ task BigQueryLoadJson { String project_id String dataset_name String output_path - String table_id + String table_suffix File? service_account_json Array[String] prep_jsons_done } - # I am going to want to have two pre-vat tables. A variant table and a genes table. They will be joined together for the vat table - # See if we can grab the annotations json directly from the gcp bucket (so pull it in as a string so it wont) + # There are two pre-vat tables. A variant table and a genes table. They are joined together for the vat table + String vat_table = "vat_" + table_suffix + String variant_transcript_table = "vat_vt_" + table_suffix + String genes_table = "vat_genes_" + table_suffix - String vat_table = "vat_" + table_id - String variant_transcript_table = "vat_vt_" + table_id - String genes_table = "vat_genes_" + table_id String vt_path = output_path + 'vt/*' String genes_path = output_path + 'genes/*' @@ -307,12 +268,12 @@ task BigQueryLoadJson { gcloud config set project ~{project_id} fi + set +e bq show --project_id ~{project_id} ~{dataset_name}.~{variant_transcript_table} > /dev/null BQ_SHOW_RC=$? - set -e - if [ $BQ_SHOW_RC -ne 0 ]; then # do we want to delete if it's still there? no shards on this part of the workflow + if [ $BQ_SHOW_RC -ne 0 ]; echo "Creating a pre-vat table ~{dataset_name}.~{variant_transcript_table}" bq --location=US mk --project_id=~{project_id} ~{dataset_name}.~{variant_transcript_table} ~{vt_schema} fi @@ -323,10 +284,8 @@ task BigQueryLoadJson { bq --location=US load --project_id=~{project_id} --source_format=NEWLINE_DELIMITED_JSON ~{dataset_name}.~{variant_transcript_table} ~{vt_path} set +e - bq show --project_id ~{project_id} ~{dataset_name}.~{genes_table} > /dev/null BQ_SHOW_RC=$? - set -e if [ $BQ_SHOW_RC -ne 0 ]; then @@ -344,15 +303,10 @@ task BigQueryLoadJson { CLUSTERING_STRING="" #--clustering_fields=$CLUSTERING_FIELD" set +e - bq show --project_id ~{project_id} ~{dataset_name}.~{vat_table} > /dev/null BQ_SHOW_RC=$? - set -e - # TODO check the below logic. Seems to be appending.....? - # TODO how do we want to be doing this? With a hash of some sort? - if [ $BQ_SHOW_RC -ne 0 ]; then echo "Creating the vat table ~{dataset_name}.~{vat_table}" bq --location=US mk --project_id=~{project_id} ~{dataset_name}.~{vat_table} ~{nirvana_schema} @@ -364,8 +318,11 @@ task BigQueryLoadJson { # Now we run a giant query in BQ to get this all in the right table and join the genes properly # Note the genes table join includes the group by to avoid the duplicates that get created from genes that span shards + # Commented out columns in the query are to be added in the next release + # We want the vat creation query to overwrite the destination table because if new data has been put into the pre-vat tables + # and this workflow has been run an additional time, we dont want duplicates being appended from the original run - bq query --nouse_legacy_sql --destination_table=~{dataset_name}.~{vat_table} --project_id=~{project_id} \ + bq query --nouse_legacy_sql --destination_table=~{dataset_name}.~{vat_table} --force=true --project_id=~{project_id} \ 'SELECT v.vid, v.transcript, @@ -401,7 +358,6 @@ task BigQueryLoadJson { # v.gnomad_max_an, # null AS gnomad_max_subpop, v.revel, - # this is the first value in spliceAI (need to validate that there will only ever be one) v.splice_ai_acceptor_gain_score, v.splice_ai_acceptor_gain_distance, v.splice_ai_acceptor_loss_score, @@ -412,7 +368,7 @@ task BigQueryLoadJson { v.splice_ai_donor_loss_distance, g.omim_phenotypes_id, g.omim_phenotypes_name, - v.clinvar_classification, # validate that we only grab lines WHERE id LIKE "RCV%" + v.clinvar_classification, v.clinvar_last_updated, v.clinvar_phenotype, FROM `~{dataset_name}.~{variant_transcript_table}` as v @@ -420,7 +376,6 @@ task BigQueryLoadJson { (SELECT gene_symbol, ANY_VALUE(gene_omim_id) AS gene_omim_id, ANY_VALUE(omim_phenotypes_id) AS omim_phenotypes_id, ANY_VALUE(omim_phenotypes_name) AS omim_phenotypes_name FROM `~{dataset_name}.~{genes_table}` group by gene_symbol) as g on v.gene_symbol = g.gene_symbol' - # TODO why do I sometimes hit an error above, but still make it to the smoke test?!?!??! Seems like the auth errors dont fail the workflow >>> # ------------------------------------------------ # Runtime settings: @@ -438,20 +393,19 @@ task BigQueryLoadJson { } } -task BigQuerySmokeTest { +task BigQuerySmokeTest { # TO BE BROKEN UP AND POTENTIALLY RUN SEPARATELY input { String project_id String dataset_name Array[File] annotation_jsons Boolean load_jsons_done File? service_account_json - String table_id + String table_suffix } - # What I want to do here is query the final table for my expected results - # This will be hardcoded for now, but in the future I may want to pull a line out of the annotations json and use thats + # Now query the final table for expected results - String vat_table = "vat_" + table_id + String vat_table = "vat_" + table_suffix String has_service_account_file = if (defined(service_account_json)) then 'true' else 'false' @@ -464,14 +418,10 @@ task BigQuerySmokeTest { gcloud config set project ~{project_id} fi - # validate the VAT table - # We will pass, or fail, a pipeline run by checking the following - - # TODO do we want to bork the pipeline if one of these following rules fail? Or simply collect the errors? + # For the validation rules that use count in SQL--the results are parsed to grab all digits in the response, which will also include error responses # ------------------------------------------------ # VALIDATION #1 - # TODO sometimes when there's an error msg, this is stripping out the #s and doing math with that like a dummy echo "VALIDATION #1" # The pipeline completed without an error message # The VAT has data in it @@ -484,7 +434,6 @@ task BigQuerySmokeTest { then echo "The VAT has no data in it" echo "Validation has failed" - # exit 1 <-- collect the errors? or fail the pipeline? else echo "The VAT has been updated" echo "Validation #1 has passed" @@ -493,22 +442,16 @@ task BigQuerySmokeTest { # ------------------------------------------------ # VALIDATION #2 # The number of passing variants in GVS matches the number of variants in the VAT. - # TODO this tests the python---what other qs should we ask here? echo "VALIDATION #2" # Please note that we are counting the number of variants in GVS, not the number of sites, which may add a difficulty to this task. - # TODO should these get broken down more so as not to test my sloppy bash over testing the data? - # TODO should I write this test in python instead?!?!? YES! I think I should!!!! ANNOTATE_JSON_VARIANT_COUNT=$(gunzip -dc ~{sep=" " annotation_jsons} | grep -o -i '"vid":' | wc -l) - # TODO do we want to also count the number of alleles in the final VCF? <-- might be worth asking Lee to clarify!!!! - echo $ANNOTATE_JSON_VARIANT_COUNT if [[ $ANNOTATE_JSON_VARIANT_COUNT -ne $BQ_VAT_VARIANT_COUNT ]] then echo "The number of variants is incorrect" echo "Validation has failed" - # exit 1 <-- collect the errors? or fail the pipeline? else echo "The number of passing variants in GVS matches the number of variants in the VAT" echo "Validation #2 has passed" @@ -516,54 +459,32 @@ task BigQuerySmokeTest { # ------------------------------------------------ # VALIDATION #3 - # Less than 5% of the variants have a non-null value in the gene field - # TODO CHECKING WITH LEE --> We dont think 5% is correct + # All variants in the TESK2 gene region (chr1:45,343,883-45,491,163) list multiple genes and those genes are always TESK2 and AL451136.1. echo "VALIDATION #3" - # Get the number of variants which have been joined - BQ_VAT_GENE_COUNT=$(bq query --nouse_legacy_sql --project_id=~{project_id} 'SELECT COUNT (DISTINCT vid) AS count FROM `~{dataset_name}.~{vat_table}` WHERE gene_symbol IS NOT NULL'| tr -dc '0-9') - echo "Get the percent" - PERCENT=$((BQ_VAT_GENE_COUNT * 100 / BQ_VAT_VARIANT_COUNT)) - echo $PERCENT - - if [[ $PERCENT -gt 25 ]] - then echo "There are too many genes" - echo "Validation has failed" - # exit 1 <-- collect the errors? or fail the pipeline? - else - echo "Less than 5% of the variants have a non-null value in the gene field" - echo "Validation #3 has passed" - fi - # ------------------------------------------------ - # VALIDATION #4 - # All variants in the TESK2 gene region (chr1:45,343,883-45,491,163) list multiple genes and those genes are always TESK2 and AL451136.1. - echo "VALIDATION #4" - # TODO ask Lee for help here. I'm not sure how to do this one? - # 'SELECT COUNT (DISTINCT vid) AS distinct_vid_count FROM `~{dataset_name}.~{vat_table}` WHERE contig = "chr1" and position >= 45343883 and position <= 45491163' + # Note: Lee has swapped this valdation to chr19 + # SELECT gene_symbol, consequence FROM `~{dataset_name}.~{vat_table}` WHERE contig = "chr19" and position >= 35740407 and position <= 35740469 and gene_symbol!="IGFLR1" and gene_symbol!="AD000671.2" + POSITIONAL_COUNT=$('SELECT COUNT (DISTINCT vid) AS distinct_vid_count FROM `~{dataset_name}.~{vat_table}` WHERE contig = "chr1" and position >= 45343883 and position <= 45491163') TESK2_COUNT=$('SELECT COUNT (DISTINCT vid) AS distinct_vid_count FROM `~{dataset_name}.~{vat_table}` WHERE contig = "chr1" and position >= 45343883 and position <= 45491163 and gene_symbol="TESK2"') AL451136_COUNT=$('SELECT COUNT (DISTINCT vid) AS distinct_vid_count FROM `~{dataset_name}.~{vat_table}` WHERE contig = "chr1" and position >= 45343883 and position <= 45491163 and gene_symbol="AL451136.1"') - echo "Still need to validate chr1" GENE_COUNT_SUM=$(( $TESK2_COUNT + $AL451136_COUNT )) - if [[ $POSITIONAL_COUNT -ne $GENE_COUNT_SUM ]] then echo "There are unexpected genes in the TESK2 region" echo "Validation has failed" - # exit 1 <-- collect the errors? or fail the pipeline? else echo "All variants in the TESK2 gene region list multiple genes and those genes are always TESK2 and AL451136.1" echo "Validation #4 has passed" fi # ------------------------------------------------ - # VALIDATION #5 + # VALIDATION #4 # If a vid has a null transcript, then the vid is only in one row of the VAT. - echo "VALIDATION #5" + echo "VALIDATION #4" # Get a count of all the rows in the vat with no transcript # Get a count of all distinct VID in vat with no transcript # Make sure they are the same - # TODO we could in the future specify which VIDs are not distinct BQ_VAT_ROWS_NO_TRANSCRIPT_COUNT=$(bq query --nouse_legacy_sql --project_id=~{project_id} 'SELECT COUNT (DISTINCT vid) AS distinct_vid_count FROM `~{dataset_name}.~{vat_table}` WHERE transcript IS NULL'| tr -dc '0-9') BQ_VAT_VARIANT_NO_TRANSCRIPT_COUNT=$(bq query --nouse_legacy_sql --project_id=~{project_id} 'SELECT COUNT(*) AS count FROM `~{dataset_name}.~{vat_table}` WHERE transcript IS NULL'| tr -dc '0-9') @@ -571,93 +492,72 @@ task BigQuerySmokeTest { then echo "The number of rows for variants with no transcripts is incorrect" echo "Validation has failed" - # exit 1 <-- collect the errors? or fail the pipeline? else echo "If a vid has a null transcript, then the vid is only in one row of the VAT" - echo "Validation #5 has passed" + echo "Validation #4 has passed" fi # ------------------------------------------------ - # VALIDATION #6 - # If a vid has any non-null transcripts then one transcript must be Ensembl (transcript_source) and canonical (is_canonical). - echo "VALIDATION #6" - # Lee is removing this for now. - echo "Lee is removing this for now" - # SELECT vid, string_agg(DISTINCT is_canonical_transcript) as canonical FROM `spec-ops-aou.anvil_100_for_testing.aou_shard_223_vat` where transcript is not null group by vid order by canonical <--there are plenty that are false - BQ_VAT_ENSEMBL_COUNT=$(bq query --nouse_legacy_sql --project_id=~{project_id} 'SELECT COUNT(*) AS count FROM `~{dataset_name}.~{vat_table}` where transcript is not null and transcript_source="Ensembl"') - BQ_VAT_TRANSCRIPT_COUNT=$(bq query --nouse_legacy_sql --project_id=~{project_id} 'SELECT COUNT(*) AS count FROM `~{dataset_name}.~{vat_table}` where transcript is not null') + # VALIDATION #5 + # There is a non-zero number of transcript fields with null values in the VAT. + echo "VALIDATION #5" - if [[ $BQ_VAT_ENSEMBL_COUNT -ne $BQ_VAT_TRANSCRIPT_COUNT ]] + if [[ $BQ_VAT_VARIANT_NO_TRANSCRIPT_COUNT -gt 0 ]] then - echo "All transcripts should be from Ensembl" echo "Validation has failed" - # exit 1 <-- collect the errors? or fail the pipeline? else - echo "If a vid has any non-null transcripts then one transcript must be Ensembl" - echo "Validation #6 has passed" - fi - - # ------------------------------------------------ - # VALIDATION #7 - # No vid may have a mix of non-null and null transcripts. - echo "VALIDATION #7" - # Get a list of all distinct vids with non-null transcripts - # Get a list of all distinct vids with no transcripts - # Make sure those lists have no intersection - - BQ_VAT_VID_OVERLAP=$(bq query --nouse_legacy_sql --project_id="spec-ops-aou" 'SELECT COUNT(vids_with_transcript_table.vid) AS count FROM (SELECT DISTINCT vid FROM `~{dataset_name}.~{vat_table}` WHERE transcript IS NULL) AS vids_no_transcript_table inner join (SELECT DISTINCT vid FROM `~{dataset_name}.~{vat_table}` WHERE transcript IS NOT NULL) AS vids_with_transcript_table on vids_with_transcript_table.vid = vids_no_transcript_table.vid') - - if [[ $BQ_VAT_VID_OVERLAP -gt 0 ]] - then echo "A vid has a mix of non-null and null transcripts" - echo "Validation has failed" - # exit 1 <-- collect the errors? or fail the pipeline? - else - echo "No vids have a mix of non-null and null transcripts" - echo "Validation #7 has passed" + echo "Validation #5 has passed" fi # ------------------------------------------------ - # VALIDATION #8 + # VALIDATION #6 # No non-nullable fields contain null values. - echo "VALIDATION #8" - # Hmmm--- the use of the vat_schema should do that for us - # Could get a count of each where _ is null - # note that the below returns nothing + # non-nullable fields: vid, contig, position, ref_allele, alt_allele, gvs_all_ac, gvs_all_an, gvs_all_af, variant_type, genomic_location + echo "VALIDATION #6" + BQ_VAT_NULL=$(bq query --nouse_legacy_sql --project_id=~{project_id} 'SELECT COUNT (DISTINCT vid) as count FROM `~{dataset_name}.~{vat_table}` WHERE vid IS NULL OR contig IS NULL OR position IS NULL OR ref_allele IS NULL OR alt_allele IS NULL OR variant_type IS NULL OR genomic_location IS NULL' - # vid, contig, position, ref_allele, alt_allele, gvs_all_ac, gvs_all_an, gvs_all_af, variant_type, genomic_location + the aou max stuff Lee still has to figure out echo $BQ_VAT_NULL if [[ $BQ_VAT_NULL -gt 0 ]] - then echo "A required value is null" + then echo "A required value is null" echo "Validation has failed" - # exit 1 <-- collect the errors? or fail the pipeline? else echo "No required values are null" - echo "Validation #8 has passed" + echo "Validation #6 has passed" fi # ------------------------------------------------ - # VALIDATION #9 - # Each key combination is unique. - echo "VALIDATION #9" + # VALIDATION #7 + # Each key combination (vid+transcript) is unique. + echo "VALIDATION #7" # get the sum of all the distinct vids where transcript is null and all the distinct transcript where transcript is not null - BQ_VAT_UNIQUE_IDS_COUNT=$(bq query --nouse_legacy_sql --project_id=~{project_id} 'SELECT COUNT(*) FROM (SELECT vid, transcript FROM `~{dataset_name}.~{vat_table}` group by vid, transcript)') - BQ_VAT_ROW_COUNT=$(bq query --nouse_legacy_sql --project_id=~{project_id} 'SELECT COUNT (*) FROM `~{dataset_name}.~{vat_table}` ') + BQ_VAT_UNIQUE_IDS_COUNT=$(bq query --nouse_legacy_sql --project_id=~{project_id} 'SELECT COUNT(*) AS count FROM (SELECT vid, transcript FROM `~{dataset_name}.~{vat_table}` group by vid, transcript)') + BQ_VAT_ROW_COUNT=$(bq query --nouse_legacy_sql --project_id=~{project_id} 'SELECT COUNT(*) AS count FROM `~{dataset_name}.~{vat_table}` ') if [ $BQ_VAT_UNIQUE_IDS_COUNT -ne $BQ_VAT_ROW_COUNT ]; - then echo "There are duplicate variant - transcript rows" - echo "Validation has failed" - # exit 1 <-- collect the errors? or fail the pipeline? + then echo "There are duplicate variant - transcript rows" + echo "Validation has failed" else: echo "Each key combination is unique" - echo "Validation #9 has passed" + echo "Validation #7 has passed" fi # ------------------------------------------------ - # FURTHER VALIDATION ?!??! - # Do I want to add additional checks that validate the mapping from the annotations json--ie count instances of 'Ensembl' in the annotations json ? - # RCA rule in clinvar data? - # check that vt and vat are the same length + + # VALIDATION #8 + # If a vid has any non-null transcripts then one transcript must be Ensembl (transcript_source). Every transcript_source is Ensembl or null. + echo "VALIDATION #8" + BQ_VAT_ENSEMBL_COUNT=$(bq query --nouse_legacy_sql --project_id=~{project_id} 'SELECT COUNT(*) AS count FROM `~{dataset_name}.~{vat_table}` where transcript is not null and transcript_source="Ensembl"') + BQ_VAT_TRANSCRIPT_COUNT=$(bq query --nouse_legacy_sql --project_id=~{project_id} 'SELECT COUNT(*) AS count FROM `~{dataset_name}.~{vat_table}` where transcript is not null') + + if [[ $BQ_VAT_ENSEMBL_COUNT -ne $BQ_VAT_TRANSCRIPT_COUNT ]] + then + echo "All transcripts should be from Ensembl" + echo "Validation has failed" + else + echo "If a vid has any non-null transcripts then one transcript must be Ensembl" + echo "Validation #8 has passed" + fi >>> # ------------------------------------------------ diff --git a/scripts/variantstore/wdl/extract/create_variant_annotation_table.py b/scripts/variantstore/wdl/extract/create_variant_annotation_table.py index 8cc92401695..0af1a92b200 100644 --- a/scripts/variantstore/wdl/extract/create_variant_annotation_table.py +++ b/scripts/variantstore/wdl/extract/create_variant_annotation_table.py @@ -9,18 +9,8 @@ import gzip import argparse -JOB_IDS = set() - -# -# CONSTANTS -# -VAT_TABLE_PREFIX = "vat_" -SAMPLES_PER_PARTITION = 4000 - -## TODO in the future do I want to map the original json key to a function!?!?!?!? - vat_nirvana_positions_dictionary = { - "position": "position", # required TODO pull this out! check how nirvana handles "when the vcf position is not just the preceeding base for the variant" + "position": "position", # required } vat_nirvana_variants_dictionary = { @@ -30,7 +20,7 @@ "alt_allele": "altAllele", # required "variant_type": "variantType", # required "genomic_location": "hgvsg", # required - "dbsnp_rsid": "dbsnp", # nullable -- TODO is this always a single val array? + "dbsnp_rsid": "dbsnp", # nullable } vat_nirvana_transcripts_dictionary = { @@ -38,15 +28,12 @@ "gene_symbol": "hgnc", # nullable "transcript_source": "source", # nullable "aa_change": "hgvsp", # nullable - "consequence": "consequence", # nullable -- this is now an array + "consequence": "consequence", # nullable "dna_change_in_transcript": "hgvsc", # nullable "exon_number": "exons", # nullable "intron_number": "introns", # nullable - # "splice_distance": "hgvsc", # nullable -- Lee has pushed this out of p0 for now "gene_id": "geneId", # nullable - # "entrez_gene_id": "geneId", # nullable - # "hgnc_gene_id": "hgncid", # nullable -- Lee has pushed this out of p0 for now - "is_canonical_transcript": "isCanonical" # nullable -- (and lets make the nulls false) + "is_canonical_transcript": "isCanonical" # nullable } vat_nirvana_gvs_alleles_dictionary = { @@ -73,27 +60,21 @@ vat_nirvana_clinvar_dictionary = { "clinvar_classification": "significance", # nullable "clinvar_last_updated": "lastUpdatedDate", # nullable - "clinvar_phenotype": "phenotypes" # nullable -- currently here: "phenotypes":["not specified"] <-- lets talk arrays! + "clinvar_phenotype": "phenotypes" # nullable } vat_nirvana_gnomad_dictionary = { "gnomad_all_af": "allAf", # nullable "gnomad_all_ac": "allAc", # nullable "gnomad_all_an": "allAn", # nullable - # "gnomad_max_af": "afrAf", # nullable THIS NEEDS MORE THAN JUST A MAPPING - # "gnomad_max_ac": "afrAc", # nullable THIS NEEDS MORE THAN JUST A MAPPING - # "gnomad_max_an": "afrAn", # nullable THIS NEEDS MORE THAN JUST A MAPPING - # "gnomad_max_subpop": "x" #TODO need to choose the correct mapping. Lee says maybe drop for now } -vat_nirvana_omim_dictionary = { # TODO or should this be vat_nirvana_genes_dictionary ? - # "hgnc_gene_id": "hgncid", # nullable genes.hgncid NOT HERE -- Lee has pushed this out of p0 for now - # "gene_omim_id": "mimNumber", # nullable genes.omim.mimNumber HARD CODED FOR NOW - "omim_phenotypes_id": "mimNumber", # nullable <-- lets talk arrays! genes.omim.phenotypes.mimNumber +vat_nirvana_omim_dictionary = { + "omim_phenotypes_id": "mimNumber", # nullable "omim_phenotypes_name": "phenotype" # nullable } -significance_ordering = [ # TODO I have lowercased this---check that this is okay. Nirvana seems to have diff cases :P +significance_ordering = [ "benign", "likely benign", "uncertain significance", @@ -111,9 +92,9 @@ ] -def make_annotated_json_row(row_position, variant_line, transcript_line): # would it be better to not pass the transcript_line since its dupe data? +def make_annotated_json_row(row_position, variant_line, transcript_line): row = {} - row["position"] = row_position # this is a required field -- do we want validation? (what about validation for all the variants_fieldnames?) + row["position"] = row_position # this is a required field for vat_variants_fieldname in vat_nirvana_variants_dictionary.keys(): # like "contig" nirvana_variants_fieldname = vat_nirvana_variants_dictionary.get(vat_variants_fieldname) @@ -144,7 +125,7 @@ def make_annotated_json_row(row_position, variant_line, transcript_line): # woul if variant_line.get("gnomad") != None: for vat_gnomad_fieldname in vat_nirvana_gnomad_dictionary.keys(): # like "gnomad_all_af" nirvana_gnomad_fieldname = vat_nirvana_gnomad_dictionary.get(vat_gnomad_fieldname) - gnomad_fieldvalue = variant_line.get("gnomad").get(nirvana_gnomad_fieldname) # not a list like the others + gnomad_fieldvalue = variant_line.get("gnomad").get(nirvana_gnomad_fieldname) row[vat_gnomad_fieldname] = gnomad_fieldvalue if variant_line.get("clinvar") != None: @@ -162,7 +143,7 @@ def make_annotated_json_row(row_position, variant_line, transcript_line): # woul phenotypes.extend(clinvar_RCV_line.get("phenotypes")) # We want to collect all the significance values and order them by the significance_ordering list # So I will loop through the significance_ordering values and check for matching values in the significance_values list and put them in a new list - ordered_significance_values = [] # how do we deal with cases issues? + ordered_significance_values = [] for value in significance_ordering: if value in significance_values: ordered_significance_values.append(value) # this adds the id to the end of the list @@ -190,12 +171,8 @@ def make_positions_json(annotated_json, output_json): positions = ijson.items(json_data, 'positions.item', use_float=True) - #TODO: filter down to Ensembl transcripts only. - # so we can no longer just check if the transcripts exist or not---need to see if they exist and then if they have transcript_source of "Ensembl" - # TODO is it better to do the transcript_source filtering here in the python, or in BQ? MAYBE BQ is cleaner? - for p in positions: - position=p['position'] # this is a required field -- do we want validation? + position=p['position'] variants=p['variants'] # row for each variant - transcript # so let's start with each variant @@ -241,14 +218,13 @@ def make_genes_json(annotated_json, output_genes_json): if gene_line.get("omim") != None: row = {} row["gene_symbol"] = gene_line.get("name") - omim_line = gene_line["omim"][0] # TODO I am making the huge assumption that we are only grabbing 1 + omim_line = gene_line["omim"][0] if len(gene_line.get("omim")) > 1: print("WARNING: An assumption about the possible count of omim values is incorrect.", gene_line.get("name"),len(gene_line.get("omim"))) row["gene_omim_id"] = omim_line.get("mimNumber") if omim_line.get("phenotypes") != None: phenotypes = omim_line["phenotypes"] for vat_omim_fieldname in omim_fieldnames: # like "mimNumber", "phenotype" - # both of these are arrays -- TODO would it be clearer if this was just hard coded? omim_field_array=[] for phenotype in phenotypes: nirvana_omim_fieldname = vat_nirvana_omim_dictionary.get(vat_omim_fieldname) @@ -265,8 +241,6 @@ def make_annotation_jsons(annotated_json, output_json, output_genes_json): # we've already read the whole file once so we have to open it again # TODO: cleanup closing of file handles make_genes_json(annotated_json, output_genes_json) - # TODO: should we be taking on the ".json.gz" to all the file names? - if __name__ == '__main__': parser = argparse.ArgumentParser(allow_abbrev=False, description='Create BQ load friendly jsons for VAT creation') @@ -274,11 +248,8 @@ def make_annotation_jsons(annotated_json, output_json, output_genes_json): parser.add_argument('--output_vt_json',type=str, help='name of the vt json', required=True) parser.add_argument('--output_genes_json',type=str, help='name of the genes json', required=True) - # Execute the parse_args() method args = parser.parse_args() make_annotation_jsons(args.annotated_json, args.output_vt_json, - args.output_genes_json) - -# TODO do I want to gsutil cp up the files into a bucket here? \ No newline at end of file + args.output_genes_json) \ No newline at end of file From 4656c46f5971a861bbd970d0eebc8581400812ea Mon Sep 17 00:00:00 2001 From: rori <6863459+RoriCremer@users.noreply.github.com> Date: Wed, 14 Jul 2021 14:06:56 -0400 Subject: [PATCH 71/73] pr review part 2 --- .../wdl/GvsSitesOnlyVCF.example.inputs.json | 13 +- scripts/variantstore/wdl/GvsSitesOnlyVCF.wdl | 21 +- .../create_variant_annotation_table.py | 5 +- ...at_genes_schema.json => genes_schema.json} | 0 .../schemas/variant_transcript_schema.json | 224 ++++++++++++++++++ 5 files changed, 243 insertions(+), 20 deletions(-) rename scripts/variantstore/wdl/schemas/{vat_genes_schema.json => genes_schema.json} (100%) create mode 100644 scripts/variantstore/wdl/schemas/variant_transcript_schema.json diff --git a/scripts/variantstore/wdl/GvsSitesOnlyVCF.example.inputs.json b/scripts/variantstore/wdl/GvsSitesOnlyVCF.example.inputs.json index 82da92b9e6b..bb8d84d0bfb 100644 --- a/scripts/variantstore/wdl/GvsSitesOnlyVCF.example.inputs.json +++ b/scripts/variantstore/wdl/GvsSitesOnlyVCF.example.inputs.json @@ -4,12 +4,11 @@ "GvsSitesOnlyVCF.output_sites_only_file_name": "hello_did_I_sites_only", "GvsSitesOnlyVCF.output_annotated_file_name": "hello_did_I_annotate", "GvsSitesOnlyVCF.nirvana_data_directory": "gs://broad-dsp-spec-ops/scratch/rcremer/Nirvana/NirvanaData.tar.gz", - "GvsSitesOnlyVCF.nirvana_schema_json_file": "gs://broad-dsp-spec-ops/scratch/rcremer/Nirvana/schemas/vat_schema.json", - "GvsSitesOnlyVCF.vat_vt_schema_json_file": "gs://broad-dsp-spec-ops/scratch/rcremer/Nirvana/schemas/vt_schema.json", - "GvsSitesOnlyVCF.vat_genes_schema_json_file": "gs://broad-dsp-spec-ops/scratch/rcremer/Nirvana/schemas/genes_schema.json", - "GvsSitesOnlyVCF.output_path": "gs://broad-dsp-spec-ops/scratch/rcremer/Nirvana/output/jul6/", - "GvsSitesOnlyVCF.table_id": "jul6", + "GvsSitesOnlyVCF.vat_schema_json_file": "gs://broad-dsp-spec-ops/scratch/rcremer/Nirvana/schemas/vat_schema.json", + "GvsSitesOnlyVCF.variant_transcript_schema_json_file": "gs://broad-dsp-spec-ops/scratch/rcremer/Nirvana/schemas/vt_schema.json", + "GvsSitesOnlyVCF.genes_schema_json_file": "gs://broad-dsp-spec-ops/scratch/rcremer/Nirvana/schemas/genes_schema.json", + "GvsSitesOnlyVCF.output_path": "gs://broad-dsp-spec-ops/scratch/rcremer/Nirvana/output/jul13/", + "GvsSitesOnlyVCF.table_suffix": "jul13", "GvsSitesOnlyVCF.project_id": "spec-ops-aou", - "GvsSitesOnlyVCF.dataset_name": "anvil_100_for_testing", - "GvsSitesOnlyVCF.service_account_json": "gs://fc-secure-e91afe60-ca52-48fa-b4a9-c76fed5a0449/keys/aou_wgs_vumc_prod.json" + "GvsSitesOnlyVCF.dataset_name": "anvil_100_for_testing" } diff --git a/scripts/variantstore/wdl/GvsSitesOnlyVCF.wdl b/scripts/variantstore/wdl/GvsSitesOnlyVCF.wdl index 53848b547d1..2a03356bf74 100644 --- a/scripts/variantstore/wdl/GvsSitesOnlyVCF.wdl +++ b/scripts/variantstore/wdl/GvsSitesOnlyVCF.wdl @@ -8,9 +8,9 @@ workflow GvsSitesOnlyVCF { String project_id String dataset_name File nirvana_data_directory - File nirvana_schema_json_file - File vat_vt_schema_json_file - File vat_genes_schema_json_file + File vat_schema_json_file + File variant_transcript_schema_json_file + File genes_schema_json_file String output_path String table_suffix @@ -38,16 +38,16 @@ workflow GvsSitesOnlyVCF { call PrepAnnotationJson { input: annotation_json = AnnotateShardedVCF.annotation_json, - output_name = "${i}.json.gz", + output_file_suffix = "${i}.json.gz", output_path = output_path, service_account_json = service_account_json, } } call BigQueryLoadJson { input: - nirvana_schema = nirvana_schema_json_file, - vt_schema = vat_vt_schema_json_file, - genes_schema = vat_genes_schema_json_file, + nirvana_schema = vat_schema_json_file, + vt_schema = variant_transcript_schema_json_file, + genes_schema = genes_schema_json_file, project_id = project_id, dataset_name = dataset_name, output_path = output_path, @@ -185,16 +185,15 @@ task AnnotateShardedVCF { task PrepAnnotationJson { input { File annotation_json - String output_name + String output_file_suffix String output_path File? service_account_json } - String output_vt_json = "vat_vt_bq_load" + output_name - String output_genes_json = "vat_genes_bq_load" + output_name + String output_vt_json = "vat_vt_bq_load" + output_file_suffix + String output_genes_json = "vat_genes_bq_load" + output_file_suffix String output_vt_gcp_path = output_path + 'vt/' String output_genes_gcp_path = output_path + 'genes/' - String output_ant_gcp_path = output_path + 'annotations/' String has_service_account_file = if (defined(service_account_json)) then 'true' else 'false' diff --git a/scripts/variantstore/wdl/extract/create_variant_annotation_table.py b/scripts/variantstore/wdl/extract/create_variant_annotation_table.py index 0af1a92b200..cb1957ec332 100644 --- a/scripts/variantstore/wdl/extract/create_variant_annotation_table.py +++ b/scripts/variantstore/wdl/extract/create_variant_annotation_table.py @@ -186,7 +186,7 @@ def make_positions_json(annotated_json, output_json): output_file.write(json_bytes) else: transcript_lines = variant.get("transcripts") - # Collect all the transcript sources and check for if they contain Ensembl <-- this might be a good place for optimization + # Collect all the transcript sources and check for if they contain Ensembl sources = [transcript.get('source') for transcript in transcript_lines] if "Ensembl" in sources: for transcript in transcript_lines: @@ -202,6 +202,7 @@ def make_positions_json(annotated_json, output_json): json_bytes = json_str.encode('utf-8') output_file.write(json_bytes) output_file.close() + json_data.close() def make_genes_json(annotated_json, output_genes_json): output_genes_file=gzip.open(output_genes_json, 'w') @@ -235,11 +236,11 @@ def make_genes_json(annotated_json, output_genes_json): json_bytes = json_str.encode('utf-8') output_genes_file.write(json_bytes) output_genes_file.close() + json_data.close() def make_annotation_jsons(annotated_json, output_json, output_genes_json): make_positions_json(annotated_json, output_json) # we've already read the whole file once so we have to open it again - # TODO: cleanup closing of file handles make_genes_json(annotated_json, output_genes_json) if __name__ == '__main__': diff --git a/scripts/variantstore/wdl/schemas/vat_genes_schema.json b/scripts/variantstore/wdl/schemas/genes_schema.json similarity index 100% rename from scripts/variantstore/wdl/schemas/vat_genes_schema.json rename to scripts/variantstore/wdl/schemas/genes_schema.json diff --git a/scripts/variantstore/wdl/schemas/variant_transcript_schema.json b/scripts/variantstore/wdl/schemas/variant_transcript_schema.json new file mode 100644 index 00000000000..0f5481d5197 --- /dev/null +++ b/scripts/variantstore/wdl/schemas/variant_transcript_schema.json @@ -0,0 +1,224 @@ +[ + { + "description": "Must be positive. Exact position for a SNP and the position before the alteration in an indel", + "name": "position", + "type": "Integer", + "mode": "Required" + }, + { + "description": "Variant ID. Unique string for identifying a variant (as produced by NIRVANA based on a spec from Broad Institute)", + "name": "vid", + "type": "String", + "mode": "Required" + }, + { + "description": "Contig names match the hg38 reference", + "name": "contig", + "type": "String", + "mode": "Required" + }, + { + "description": "base(s). This should always be one base for SNPs and insertions. More than one base for deletions", + "name": "ref_allele", + "type": "String", + "mode": "Required" + }, + { + "description": "base(s). This should always be one base for SNPs and deletions. More than one base for insertions", + "name": "alt_allele", + "type": "String", + "mode": "Required" + }, + { + "description": "DNA change type (HGVS)", + "name": "variant_type", + "type": "String", + "mode": "Required" + }, + { + "description": "HGVS g. nomenclature Variant location", + "name": "genomic_location", + "type": "String", + "mode": "Required" + }, + { + "description": "rsID", + "name": "dbsnp_rsid", + "type": "String", + "mode": "Repeated" + }, + { + "description": "Transcript ID. Null indicates that this variant does not overlap any transcripts", + "name": "transcript", + "type": "String", + "mode": "Nullable" + }, + { + "description": "Gene symbol. A variant can have more than one associated gene symbol, since about 3% of genes do overlap", + "name": "gene_symbol", + "type": "String", + "mode": "Nullable" + }, + { + "description": "", + "name": "transcript_source", + "type": "String", + "mode": "Nullable" + }, + { + "description": "HGVS p. nomenclature; Amino acid change", + "name": "aa_change", + "type": "String", + "mode": "Nullable" + }, + { + "description": "Amino acid change type TODO check with Lee about why this json thinks its Repeated not nullable", + "name": "consequence", + "type": "String", + "mode": "Repeated" + }, + { + "description": "HGVS c. nomenclature; DNA change in transcript space", + "name": "dna_change_in_transcript", + "type": "String", + "mode": "Nullable" + }, + { + "description": "Exon number", + "name": "exon_number", + "type": "String", + "mode": "Nullable" + }, + { + "description": "Intron number", + "name": "intron_number", + "type": "String", + "mode": "Nullable" + }, + { + "description": "Gene ID for the transcript", + "name": "gene_id", + "type": "String", + "mode": "Nullable" + }, + { + "description": "Primary Transcript ID", + "name": "is_canonical_transcript", + "type": "Boolean", + "mode": "Nullable" + }, + { + "description": "AC TODO -- this needs to be added back and swapped to required -- Lee said this was a string?", + "name": "gvs_all_ac", + "type": "Integer", + "mode": "Nullable" + }, + { + "description": "AN TODO -- this needs to be added back and swapped to required", + "name": "gvs_all_an", + "type": "Integer", + "mode": "Nullable" + }, + { + "description": "AF TODO -- this needs to be added back and swapped to required -- Lee said this was a Float?", + "name": "gvs_all_af", + "type": "INTEGER", + "mode": "Nullable" + }, + { + "description": "REVEL", + "name": "revel", + "type": "FLOAT", + "mode": "Nullable" + }, + { + "description": "Slice AI", + "name": "splice_ai_acceptor_gain_score", + "type": "Float", + "mode": "Nullable" + }, + { + "description": "Slice AI", + "name": "splice_ai_acceptor_gain_distance", + "type": "Integer", + "mode": "Nullable" + }, + { + "description": "Slice AI", + "name": "splice_ai_acceptor_loss_score", + "type": "Float", + "mode": "Nullable" + }, + { + "description": "Slice AI", + "name": "splice_ai_acceptor_loss_distance", + "type": "Integer", + "mode": "Nullable" + }, + { + "description": "Slice AI", + "name": "splice_ai_donor_gain_score", + "type": "Float", + "mode": "Nullable" + }, + { + "description": "Slice AI", + "name": "splice_ai_donor_gain_distance", + "type": "Integer", + "mode": "Nullable" + }, + { + "description": "Slice AI", + "name": "splice_ai_donor_loss_score", + "type": "Float", + "mode": "Nullable" + }, + { + "description": "Slice AI", + "name": "splice_ai_donor_loss_distance", + "type": "Integer", + "mode": "Nullable" + }, + { + "description": "ClinVar Id for Validation", + "name": "clinvar_id", + "type": "String", + "mode": "Repeated" + }, + { + "description": "ClinVar Classification", + "name": "clinvar_classification", + "type": "String", + "mode": "Repeated" + }, + { + "description": "ClinVar Classification Date", + "name": "clinvar_last_updated", + "type": "Date", + "mode": "Nullable" + }, + { + "description": "ClinVar Disease Name", + "name": "clinvar_phenotype", + "type": "String", + "mode": "Repeated" + }, + { + "description": "gnomAD: 'Total' frequency", + "name": "gnomad_all_af", + "type": "Float", + "mode": "Nullable" + }, + { + "description": "gnomAD: 'Total' allele count", + "name": "gnomad_all_ac", + "type": "Integer", + "mode": "Nullable" + }, + { + "description": "gnomAD: 'Total' allele number", + "name": "gnomad_all_an", + "type": "Integer", + "mode": "Nullable" + } +] From 68288293f25eded9345fd1d685d67ff0a16a652e Mon Sep 17 00:00:00 2001 From: rori <6863459+RoriCremer@users.noreply.github.com> Date: Wed, 14 Jul 2021 15:10:29 -0400 Subject: [PATCH 72/73] typo --- scripts/variantstore/wdl/GvsSitesOnlyVCF.wdl | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/scripts/variantstore/wdl/GvsSitesOnlyVCF.wdl b/scripts/variantstore/wdl/GvsSitesOnlyVCF.wdl index 2a03356bf74..738c3386037 100644 --- a/scripts/variantstore/wdl/GvsSitesOnlyVCF.wdl +++ b/scripts/variantstore/wdl/GvsSitesOnlyVCF.wdl @@ -272,7 +272,7 @@ task BigQueryLoadJson { BQ_SHOW_RC=$? set -e - if [ $BQ_SHOW_RC -ne 0 ]; + if [ $BQ_SHOW_RC -ne 0 ]; then echo "Creating a pre-vat table ~{dataset_name}.~{variant_transcript_table}" bq --location=US mk --project_id=~{project_id} ~{dataset_name}.~{variant_transcript_table} ~{vt_schema} fi @@ -321,7 +321,7 @@ task BigQueryLoadJson { # We want the vat creation query to overwrite the destination table because if new data has been put into the pre-vat tables # and this workflow has been run an additional time, we dont want duplicates being appended from the original run - bq query --nouse_legacy_sql --destination_table=~{dataset_name}.~{vat_table} --force=true --project_id=~{project_id} \ + bq query --nouse_legacy_sql --destination_table=~{dataset_name}.~{vat_table} --replace --project_id=~{project_id} \ 'SELECT v.vid, v.transcript, From 83a58580ed7f7efc0cbde3440379d4c1fde99005 Mon Sep 17 00:00:00 2001 From: rori <6863459+RoriCremer@users.noreply.github.com> Date: Wed, 14 Jul 2021 20:37:50 -0400 Subject: [PATCH 73/73] smoketest tune up --- scripts/variantstore/wdl/GvsSitesOnlyVCF.wdl | 11 ++++++----- scripts/variantstore/wdl/schemas/vat_schema.json | 14 +++++++------- 2 files changed, 13 insertions(+), 12 deletions(-) diff --git a/scripts/variantstore/wdl/GvsSitesOnlyVCF.wdl b/scripts/variantstore/wdl/GvsSitesOnlyVCF.wdl index 738c3386037..7103d2611b8 100644 --- a/scripts/variantstore/wdl/GvsSitesOnlyVCF.wdl +++ b/scripts/variantstore/wdl/GvsSitesOnlyVCF.wdl @@ -464,9 +464,9 @@ task BigQuerySmokeTest { # TO BE BROKEN UP AND POTENTIALLY RUN SEPARATELY # Note: Lee has swapped this valdation to chr19 # SELECT gene_symbol, consequence FROM `~{dataset_name}.~{vat_table}` WHERE contig = "chr19" and position >= 35740407 and position <= 35740469 and gene_symbol!="IGFLR1" and gene_symbol!="AD000671.2" - POSITIONAL_COUNT=$('SELECT COUNT (DISTINCT vid) AS distinct_vid_count FROM `~{dataset_name}.~{vat_table}` WHERE contig = "chr1" and position >= 45343883 and position <= 45491163') - TESK2_COUNT=$('SELECT COUNT (DISTINCT vid) AS distinct_vid_count FROM `~{dataset_name}.~{vat_table}` WHERE contig = "chr1" and position >= 45343883 and position <= 45491163 and gene_symbol="TESK2"') - AL451136_COUNT=$('SELECT COUNT (DISTINCT vid) AS distinct_vid_count FROM `~{dataset_name}.~{vat_table}` WHERE contig = "chr1" and position >= 45343883 and position <= 45491163 and gene_symbol="AL451136.1"') + POSITIONAL_COUNT=$(bq query --nouse_legacy_sql --project_id=~{project_id} 'SELECT COUNT (DISTINCT vid) AS distinct_vid_count FROM `~{dataset_name}.~{vat_table}` WHERE contig = "chr1" and position >= 45343883 and position <= 45491163'| tr -dc '0-9') + TESK2_COUNT=$(bq query --nouse_legacy_sql --project_id=~{project_id} 'SELECT COUNT (DISTINCT vid) AS distinct_vid_count FROM `~{dataset_name}.~{vat_table}` WHERE contig = "chr1" and position >= 45343883 and position <= 45491163 and gene_symbol="TESK2"'| tr -dc '0-9') + AL451136_COUNT=$(bq query --nouse_legacy_sql --project_id=~{project_id} 'SELECT COUNT (DISTINCT vid) AS distinct_vid_count FROM `~{dataset_name}.~{vat_table}` WHERE contig = "chr1" and position >= 45343883 and position <= 45491163 and gene_symbol="AL451136.1"'| tr -dc '0-9') GENE_COUNT_SUM=$(( $TESK2_COUNT + $AL451136_COUNT )) if [[ $POSITIONAL_COUNT -ne $GENE_COUNT_SUM ]] @@ -514,11 +514,12 @@ task BigQuerySmokeTest { # TO BE BROKEN UP AND POTENTIALLY RUN SEPARATELY # non-nullable fields: vid, contig, position, ref_allele, alt_allele, gvs_all_ac, gvs_all_an, gvs_all_af, variant_type, genomic_location echo "VALIDATION #6" - BQ_VAT_NULL=$(bq query --nouse_legacy_sql --project_id=~{project_id} 'SELECT COUNT (DISTINCT vid) as count FROM `~{dataset_name}.~{vat_table}` WHERE vid IS NULL OR contig IS NULL OR position IS NULL OR ref_allele IS NULL OR alt_allele IS NULL OR variant_type IS NULL OR genomic_location IS NULL' + BQ_VAT_NULL=$(bq query --nouse_legacy_sql --project_id=~{project_id} 'SELECT COUNT (DISTINCT vid) as count FROM `~{dataset_name}.~{vat_table}` WHERE vid IS NULL OR contig IS NULL OR position IS NULL OR ref_allele IS NULL OR alt_allele IS NULL OR variant_type IS NULL OR genomic_location IS NULL') echo $BQ_VAT_NULL if [[ $BQ_VAT_NULL -gt 0 ]] - then echo "A required value is null" + then + echo "A required value is null" echo "Validation has failed" else echo "No required values are null" diff --git a/scripts/variantstore/wdl/schemas/vat_schema.json b/scripts/variantstore/wdl/schemas/vat_schema.json index b734e431caf..49a7211fad3 100644 --- a/scripts/variantstore/wdl/schemas/vat_schema.json +++ b/scripts/variantstore/wdl/schemas/vat_schema.json @@ -108,22 +108,22 @@ "mode": "Nullable" }, { - "description": "AC TODO -- this needs to be added back and swapped to required -- Lee said this was a string?", + "description": "AC", "name": "gvs_all_ac", "type": "Integer", - "mode": "Nullable" + "mode": "Required" }, { - "description": "AN TODO -- this needs to be added back and swapped to required", + "description": "AN", "name": "gvs_all_an", "type": "Integer", - "mode": "Nullable" + "mode": "Required" }, { - "description": "AF TODO -- this needs to be added back and swapped to required -- Lee said this was a Float?", + "description": "AF", "name": "gvs_all_af", - "type": "INTEGER", - "mode": "Nullable" + "type": "Float", + "mode": "Required" }, { "description": "REVEL",