Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Staging -> master #1198

Merged
merged 32 commits into from
Feb 7, 2024
Merged

Staging -> master #1198

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
32 commits
Select commit Hold shift + click to select a range
5702559
update paths to input files
jessicaway Oct 25, 2023
5c57a21
update jg sample map
jessicaway Oct 25, 2023
45f6884
Km buildindices docs (#1158)
kayleemathews Dec 20, 2023
7662600
Lk pd2448 upstools (#1150)
ekiernan Dec 20, 2023
83f5ece
PD-2435 Test bwa-mem2 step and run Intel distributed BWA-MEM2 (#1147)
aawdeh Dec 20, 2023
f10e0a6
Merge pull request #1162 from broadinstitute/develop
jessicaway Jan 3, 2024
dbc83cf
Merge branch 'develop' into jw_fix_jg_plumbing_test
jessicaway Jan 3, 2024
47e49b3
Lk pd2453 add bb tag (#1161)
ekiernan Jan 4, 2024
6fb03c1
km paired-tag docs (#1165)
kayleemathews Jan 5, 2024
b2b48c7
Merge branch 'develop' into jw_fix_jg_plumbing_test
jessicaway Jan 5, 2024
4ea11fb
Merge pull request #1166 from broadinstitute/jw_fix_jg_plumbing_test
jessicaway Jan 5, 2024
15a924f
Np jprb pd 2353 multiple star rsolo align (#1164)
nikellepetrillo Jan 8, 2024
59ae4d4
Np update multiome sci test (#1167)
nikellepetrillo Jan 9, 2024
23df266
Merge pull request #1169 from broadinstitute/develop
nikellepetrillo Jan 9, 2024
1279a69
PD-2422 BICAN_Optimus_2nymxis_Oct_2023 (#1152)
aawdeh Jan 12, 2024
f3e8d6e
Np multimapper param starsolo (#1172)
nikellepetrillo Jan 16, 2024
e83f3fe
added exit code to CompareTabix (#1174)
ekiernan Jan 16, 2024
3e86adb
Lk pd 2452 add read length check (#1171)
ekiernan Jan 18, 2024
4602a88
Lk pd 2464 batch methylome (#1181)
ekiernan Jan 26, 2024
9b1f344
Np edit resources needed for bwa task / add logic to compareBams (#1183)
nikellepetrillo Jan 29, 2024
38200f5
PD-2483 (#1182)
rsc3 Jan 30, 2024
fda51df
PD-2476: Add task before fastqprocess to find number of splits (#1178)
aawdeh Jan 31, 2024
715a1ad
removed space (#1184)
ekiernan Feb 1, 2024
ff75140
Lk pd 2455 pairedtag parsebarcodes (#1186)
ekiernan Feb 1, 2024
0d7a553
Np move snm3c from beta pipelines (#1185)
nikellepetrillo Feb 1, 2024
6c6aaae
Km snm3c overview doc (#1179)
kayleemathews Feb 1, 2024
fc370b9
Np fix snm3c test (#1190)
nikellepetrillo Feb 2, 2024
91497b9
Merge pull request #1189 from broadinstitute/develop
nikellepetrillo Feb 2, 2024
8a9e240
Np fix verify task (#1196)
nikellepetrillo Feb 5, 2024
45928e3
BGE settings for Reblocking and JointCalling pipelines (#1076)
meganshand Feb 6, 2024
899243a
Merge pull request #1197 from broadinstitute/develop
nikellepetrillo Feb 6, 2024
25ba01a
conflicts
nikellepetrillo Feb 6, 2024
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
6 changes: 6 additions & 0 deletions pipelines/broad/dna_seq/germline/joint_genotyping/JointGenotyping.changelog.md
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -1,3 +1,9 @@
# 1.6.9
2023-09-08 (Date of Last Commit)

* Added option to run VETS instead of VQSR for filtering
* Added option to hard filter sites outside of provided interval list

# 1.6.8
2023-06-29 (Date of Last Commit)

Expand Down
252 changes: 140 additions & 112 deletions pipelines/broad/dna_seq/germline/joint_genotyping/JointGenotyping.wdl
View file
Open in desktop

Large diffs are not rendered by default.

5 changes: 5 additions & 0 deletions ...line/joint_genotyping/UltimaGenomics/UltimaGenomicsJointGenotyping.changelog.md
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -1,3 +1,8 @@
# 1.1.5
2023-09-08 (Date of Last Commit)

* Added option to hard filter sites outside of provided interval list to HardFilterAndMakeSitesOnlyVcf task

# 1.1.4
2023-06-29 (Date of Last Commit)

Expand Down
2 changes: 1 addition & 1 deletion .../broad/dna_seq/germline/joint_genotyping/UltimaGenomics/UltimaGenomicsJointGenotyping.wdl
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -11,7 +11,7 @@ import "../../../../../../tasks/broad/UltimaGenomicsGermlineFilteringThreshold.w
# For choosing a filtering threshold (where on the ROC curve to filter) a sample with truth data is required.
workflow UltimaGenomicsJointGenotyping {

String pipeline_version = "1.1.4"
String pipeline_version = "1.1.5"

input {
File unpadded_intervals_file
Expand Down
5 changes: 5 additions & 0 deletions .../joint_genotyping/by_chromosome/JointGenotypingByChromosomePartOne.changelog.md
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -1,3 +1,8 @@
# 1.4.11
2023-09-08 (Date of Last Commit)

* Added option to hard filter sites outside of provided interval list to HardFilterAndMakeSitesOnlyVcf task

# 1.4.10
2023-06-29 (Date of Last Commit)

Expand Down
2 changes: 1 addition & 1 deletion ...ad/dna_seq/germline/joint_genotyping/by_chromosome/JointGenotypingByChromosomePartOne.wdl
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -5,7 +5,7 @@ import "../../../../../../tasks/broad/JointGenotypingTasks.wdl" as Tasks
# Joint Genotyping for hg38 Exomes and Whole Genomes (has not been tested on hg19)
workflow JointGenotypingByChromosomePartOne {

String pipeline_version = "1.4.10"
String pipeline_version = "1.4.11"

input {
File unpadded_intervals_file
Expand Down
5 changes: 5 additions & 0 deletions .../joint_genotyping/by_chromosome/JointGenotypingByChromosomePartTwo.changelog.md
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -1,3 +1,8 @@
# 1.4.10
2023-09-08 (Date of Last Commit)

* Added option to hard filter sites outside of provided interval list to HardFilterAndMakeSitesOnlyVcf task

# 1.4.9
2023-06-29 (Date of Last Commit)

Expand Down
2 changes: 1 addition & 1 deletion ...ad/dna_seq/germline/joint_genotyping/by_chromosome/JointGenotypingByChromosomePartTwo.wdl
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -5,7 +5,7 @@ import "../../../../../../tasks/broad/JointGenotypingTasks.wdl" as Tasks
# Joint Genotyping for hg38 Exomes and Whole Genomes (has not been tested on hg19)
workflow JointGenotypingByChromosomePartTwo {

String pipeline_version = "1.4.9"
String pipeline_version = "1.4.10"

input {
String callset_name
Expand Down
4 changes: 2 additions & 2 deletions pipelines/broad/dna_seq/germline/joint_genotyping/exome/JointGenotyping.inputs.json
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -9,8 +9,8 @@
"JointGenotyping.snp_recalibration_annotation_values": ["AS_QD", "AS_MQRankSum", "AS_ReadPosRankSum", "AS_FS", "AS_MQ", "AS_SOR"],
"JointGenotyping.indel_recalibration_tranche_values": ["100.0", "99.95", "99.9", "99.5", "99.0", "97.0", "96.0", "95.0", "94.0", "93.5", "93.0", "92.0", "91.0", "90.0"],
"JointGenotyping.indel_recalibration_annotation_values": ["AS_FS", "AS_ReadPosRankSum", "AS_MQRankSum", "AS_QD", "AS_SOR"],
"JointGenotyping.snp_filter_level": 99.7,
"JointGenotyping.indel_filter_level": 95.0,
"JointGenotyping.vqsr_snp_filter_level": 99.7,
"JointGenotyping.vqsr_indel_filter_level": 95.0,
"JointGenotyping.snp_vqsr_downsampleFactor": 10,
"JointGenotyping.hapmap_resource_vcf": "gs://gcp-public-data--broad-references/hg38/v0/hapmap_3.3.hg38.vcf.gz",
"JointGenotyping.omni_resource_vcf": "gs://gcp-public-data--broad-references/hg38/v0/1000G_omni2.5.hg38.vcf.gz",
Expand Down
4 changes: 2 additions & 2 deletions ...dna_seq/germline/joint_genotyping/exome/test_inputs/Plumbing/gather_vcfs_high_memory.json
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -9,8 +9,8 @@
"JointGenotyping.snp_recalibration_annotation_values": ["AS_QD", "AS_MQRankSum", "AS_ReadPosRankSum", "AS_FS", "AS_MQ", "AS_SOR"],
"JointGenotyping.indel_recalibration_tranche_values": ["100.0", "99.95", "99.9", "99.5", "99.0", "97.0", "96.0", "95.0", "94.0", "93.5", "93.0", "92.0", "91.0", "90.0"],
"JointGenotyping.indel_recalibration_annotation_values": ["AS_FS", "AS_ReadPosRankSum", "AS_MQRankSum", "AS_QD", "AS_SOR"],
"JointGenotyping.snp_filter_level": 99.7,
"JointGenotyping.indel_filter_level": 95.0,
"JointGenotyping.vqsr_snp_filter_level": 99.7,
"JointGenotyping.vqsr_indel_filter_level": 95.0,
"JointGenotyping.snp_vqsr_downsampleFactor": 1,
"JointGenotyping.hapmap_resource_vcf": "gs://gcp-public-data--broad-references/hg38/v0/hapmap_3.3.hg38.vcf.gz",
"JointGenotyping.omni_resource_vcf": "gs://gcp-public-data--broad-references/hg38/v0/1000G_omni2.5.hg38.vcf.gz",
Expand Down
4 changes: 2 additions & 2 deletions .../dna_seq/germline/joint_genotyping/exome/test_inputs/Plumbing/gather_vcfs_low_memory.json
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -9,8 +9,8 @@
"JointGenotyping.snp_recalibration_annotation_values": ["AS_QD", "AS_MQRankSum", "AS_ReadPosRankSum", "AS_FS", "AS_MQ", "AS_SOR"],
"JointGenotyping.indel_recalibration_tranche_values": ["100.0", "99.95", "99.9", "99.5", "99.0", "97.0", "96.0", "95.0", "94.0", "93.5", "93.0", "92.0", "91.0", "90.0"],
"JointGenotyping.indel_recalibration_annotation_values": ["AS_FS", "AS_ReadPosRankSum", "AS_MQRankSum", "AS_QD", "AS_SOR"],
"JointGenotyping.snp_filter_level": 99.7,
"JointGenotyping.indel_filter_level": 95.0,
"JointGenotyping.vqsr_snp_filter_level": 99.7,
"JointGenotyping.vqsr_indel_filter_level": 95.0,
"JointGenotyping.snp_vqsr_downsampleFactor": 10,
"JointGenotyping.hapmap_resource_vcf": "gs://gcp-public-data--broad-references/hg38/v0/hapmap_3.3.hg38.vcf.gz",
"JointGenotyping.omni_resource_vcf": "gs://gcp-public-data--broad-references/hg38/v0/1000G_omni2.5.hg38.vcf.gz",
Expand Down
4 changes: 2 additions & 2 deletions pipelines/broad/dna_seq/germline/joint_genotyping/exome/test_inputs/Plumbing/gnarly.json
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -9,8 +9,8 @@
"JointGenotyping.snp_recalibration_annotation_values": ["QD", "MQRankSum", "ReadPosRankSum", "FS", "SOR"],
"JointGenotyping.indel_recalibration_tranche_values": ["100.0", "99.95", "99.9", "99.5", "99.0", "97.0", "96.0", "95.0", "94.0", "93.5", "93.0", "92.0", "91.0", "90.0"],
"JointGenotyping.indel_recalibration_annotation_values": ["FS", "ReadPosRankSum", "MQRankSum", "QD", "SOR"],
"JointGenotyping.snp_filter_level": 99.7,
"JointGenotyping.indel_filter_level": 95.0,
"JointGenotyping.vqsr_snp_filter_level": 99.7,
"JointGenotyping.vqsr_indel_filter_level": 95.0,
"JointGenotyping.snp_vqsr_downsampleFactor": 10,
"JointGenotyping.hapmap_resource_vcf": "gs://gcp-public-data--broad-references/hg38/v0/hapmap_3.3.hg38.vcf.gz",
"JointGenotyping.omni_resource_vcf": "gs://gcp-public-data--broad-references/hg38/v0/1000G_omni2.5.hg38.vcf.gz",
Expand Down
4 changes: 2 additions & 2 deletions .../dna_seq/germline/joint_genotyping/exome/test_inputs/Plumbing/shard_vcfs_high_memory.json
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -9,8 +9,8 @@
"JointGenotyping.snp_recalibration_annotation_values": ["AS_QD", "AS_MQRankSum", "AS_ReadPosRankSum", "AS_FS", "AS_MQ", "AS_SOR"],
"JointGenotyping.indel_recalibration_tranche_values": ["100.0", "99.95", "99.9", "99.5", "99.0", "97.0", "96.0", "95.0", "94.0", "93.5", "93.0", "92.0", "91.0", "90.0"],
"JointGenotyping.indel_recalibration_annotation_values": ["AS_FS", "AS_ReadPosRankSum", "AS_MQRankSum", "AS_QD", "AS_SOR"],
"JointGenotyping.snp_filter_level": 99.7,
"JointGenotyping.indel_filter_level": 95.0,
"JointGenotyping.vqsr_snp_filter_level": 99.7,
"JointGenotyping.vqsr_indel_filter_level": 95.0,
"JointGenotyping.snp_vqsr_downsampleFactor": 1,
"JointGenotyping.hapmap_resource_vcf": "gs://gcp-public-data--broad-references/hg38/v0/hapmap_3.3.hg38.vcf.gz",
"JointGenotyping.omni_resource_vcf": "gs://gcp-public-data--broad-references/hg38/v0/1000G_omni2.5.hg38.vcf.gz",
Expand Down
4 changes: 2 additions & 2 deletions ...d/dna_seq/germline/joint_genotyping/exome/test_inputs/Plumbing/shard_vcfs_low_memory.json
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -9,8 +9,8 @@
"JointGenotyping.snp_recalibration_annotation_values": ["AS_QD", "AS_MQRankSum", "AS_ReadPosRankSum", "AS_FS", "AS_MQ", "AS_SOR"],
"JointGenotyping.indel_recalibration_tranche_values": ["100.0", "99.95", "99.9", "99.5", "99.0", "97.0", "96.0", "95.0", "94.0", "93.5", "93.0", "92.0", "91.0", "90.0"],
"JointGenotyping.indel_recalibration_annotation_values": ["AS_FS", "AS_ReadPosRankSum", "AS_MQRankSum", "AS_QD", "AS_SOR"],
"JointGenotyping.snp_filter_level": 99.7,
"JointGenotyping.indel_filter_level": 95.0,
"JointGenotyping.vqsr_snp_filter_level": 99.7,
"JointGenotyping.vqsr_indel_filter_level": 95.0,
"JointGenotyping.snp_vqsr_downsampleFactor": 10,
"JointGenotyping.hapmap_resource_vcf": "gs://gcp-public-data--broad-references/hg38/v0/hapmap_3.3.hg38.vcf.gz",
"JointGenotyping.omni_resource_vcf": "gs://gcp-public-data--broad-references/hg38/v0/1000G_omni2.5.hg38.vcf.gz",
Expand Down
4 changes: 2 additions & 2 deletions ...a_seq/germline/joint_genotyping/exome/test_inputs/Scientific/gather_vcfs_high_memory.json
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -9,8 +9,8 @@
"JointGenotyping.snp_recalibration_annotation_values": ["AS_QD", "AS_MQRankSum", "AS_ReadPosRankSum", "AS_FS", "AS_MQ", "AS_SOR"],
"JointGenotyping.indel_recalibration_tranche_values": ["100.0", "99.95", "99.9", "99.5", "99.0", "97.0", "96.0", "95.0", "94.0", "93.5", "93.0", "92.0", "91.0", "90.0"],
"JointGenotyping.indel_recalibration_annotation_values": ["AS_FS", "AS_ReadPosRankSum", "AS_MQRankSum", "AS_QD", "AS_SOR"],
"JointGenotyping.snp_filter_level": 99.7,
"JointGenotyping.indel_filter_level": 95.0,
"JointGenotyping.vqsr_snp_filter_level": 99.7,
"JointGenotyping.vqsr_indel_filter_level": 95.0,
"JointGenotyping.snp_vqsr_downsampleFactor": 1,
"JointGenotyping.hapmap_resource_vcf": "gs://gcp-public-data--broad-references/hg38/v0/hapmap_3.3.hg38.vcf.gz",
"JointGenotyping.omni_resource_vcf": "gs://gcp-public-data--broad-references/hg38/v0/1000G_omni2.5.hg38.vcf.gz",
Expand Down
4 changes: 2 additions & 2 deletions ...na_seq/germline/joint_genotyping/exome/test_inputs/Scientific/gather_vcfs_low_memory.json
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -9,8 +9,8 @@
"JointGenotyping.snp_recalibration_annotation_values": ["AS_QD", "AS_MQRankSum", "AS_ReadPosRankSum", "AS_FS", "AS_MQ", "AS_SOR"],
"JointGenotyping.indel_recalibration_tranche_values": ["100.0", "99.95", "99.9", "99.5", "99.0", "97.0", "96.0", "95.0", "94.0", "93.5", "93.0", "92.0", "91.0", "90.0"],
"JointGenotyping.indel_recalibration_annotation_values": ["AS_FS", "AS_ReadPosRankSum", "AS_MQRankSum", "AS_QD", "AS_SOR"],
"JointGenotyping.snp_filter_level": 99.7,
"JointGenotyping.indel_filter_level": 95.0,
"JointGenotyping.vqsr_snp_filter_level": 99.7,
"JointGenotyping.vqsr_indel_filter_level": 95.0,
"JointGenotyping.snp_vqsr_downsampleFactor": 10,
"JointGenotyping.hapmap_resource_vcf": "gs://gcp-public-data--broad-references/hg38/v0/hapmap_3.3.hg38.vcf.gz",
"JointGenotyping.omni_resource_vcf": "gs://gcp-public-data--broad-references/hg38/v0/1000G_omni2.5.hg38.vcf.gz",
Expand Down
4 changes: 2 additions & 2 deletions ...na_seq/germline/joint_genotyping/exome/test_inputs/Scientific/shard_vcfs_high_memory.json
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -9,8 +9,8 @@
"JointGenotyping.snp_recalibration_annotation_values": ["AS_QD", "AS_MQRankSum", "AS_ReadPosRankSum", "AS_FS", "AS_MQ", "AS_SOR"],
"JointGenotyping.indel_recalibration_tranche_values": ["100.0", "99.95", "99.9", "99.5", "99.0", "97.0", "96.0", "95.0", "94.0", "93.5", "93.0", "92.0", "91.0", "90.0"],
"JointGenotyping.indel_recalibration_annotation_values": ["AS_FS", "AS_ReadPosRankSum", "AS_MQRankSum", "AS_QD", "AS_SOR"],
"JointGenotyping.snp_filter_level": 99.7,
"JointGenotyping.indel_filter_level": 95.0,
"JointGenotyping.vqsr_snp_filter_level": 99.7,
"JointGenotyping.vqsr_indel_filter_level": 95.0,
"JointGenotyping.snp_vqsr_downsampleFactor": 1,
"JointGenotyping.hapmap_resource_vcf": "gs://gcp-public-data--broad-references/hg38/v0/hapmap_3.3.hg38.vcf.gz",
"JointGenotyping.omni_resource_vcf": "gs://gcp-public-data--broad-references/hg38/v0/1000G_omni2.5.hg38.vcf.gz",
Expand Down
4 changes: 2 additions & 2 deletions ...dna_seq/germline/joint_genotyping/exome/test_inputs/Scientific/shard_vcfs_low_memory.json
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -9,8 +9,8 @@
"JointGenotyping.snp_recalibration_annotation_values": ["AS_QD", "AS_MQRankSum", "AS_ReadPosRankSum", "AS_FS", "AS_MQ", "AS_SOR"],
"JointGenotyping.indel_recalibration_tranche_values": ["100.0", "99.95", "99.9", "99.5", "99.0", "97.0", "96.0", "95.0", "94.0", "93.5", "93.0", "92.0", "91.0", "90.0"],
"JointGenotyping.indel_recalibration_annotation_values": ["AS_FS", "AS_ReadPosRankSum", "AS_MQRankSum", "AS_QD", "AS_SOR"],
"JointGenotyping.snp_filter_level": 99.7,
"JointGenotyping.indel_filter_level": 95.0,
"JointGenotyping.vqsr_snp_filter_level": 99.7,
"JointGenotyping.vqsr_indel_filter_level": 95.0,
"JointGenotyping.snp_vqsr_downsampleFactor": 10,
"JointGenotyping.hapmap_resource_vcf": "gs://gcp-public-data--broad-references/hg38/v0/hapmap_3.3.hg38.vcf.gz",
"JointGenotyping.omni_resource_vcf": "gs://gcp-public-data--broad-references/hg38/v0/1000G_omni2.5.hg38.vcf.gz",
Expand Down
7 changes: 7 additions & 0 deletions ...nes/broad/dna_seq/germline/joint_genotyping/reblocking/ReblockGVCF.changelog.md
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -1,3 +1,10 @@
# 2.1.10
2023-12-14 (Date of Last Commit)

* Updated GATK for Reblock task to version 4.5.0.0
* Added options to Reblock task to remove annotations and move filters to genotype level


# 2.1.9
2023-12-08 (Date of Last Commit)

Expand Down
9 changes: 7 additions & 2 deletions pipelines/broad/dna_seq/germline/joint_genotyping/reblocking/ReblockGVCF.wdl
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -5,7 +5,7 @@ import "../../../../../../tasks/broad/Qc.wdl" as QC

workflow ReblockGVCF {

String pipeline_version = "2.1.9"
String pipeline_version = "2.1.10"


input {
Expand All @@ -17,9 +17,12 @@ workflow ReblockGVCF {
File ref_fasta_index
Float? tree_score_cutoff
String? annotations_to_keep_command
String? annotations_to_remove_command
Boolean? move_filters_to_genotypes
String gvcf_file_extension = ".g.vcf.gz"
}

String gvcf_basename = basename(gvcf, ".g.vcf.gz")
String gvcf_basename = basename(gvcf, gvcf_file_extension)

call Calling.Reblock as Reblock {
input:
Expand All @@ -30,6 +33,8 @@ workflow ReblockGVCF {
ref_dict = ref_dict,
tree_score_cutoff = tree_score_cutoff,
annotations_to_keep_command = annotations_to_keep_command,
annotations_to_remove_command = annotations_to_remove_command,
move_filters_to_genotypes = move_filters_to_genotypes,
output_vcf_filename = gvcf_basename + ".rb.g.vcf.gz"
}

Expand Down
11 changes: 11 additions & 0 deletions ...road/dna_seq/germline/joint_genotyping/reblocking/test_inputs/Scientific/NA12878.bge.json
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -0,0 +1,11 @@
{
"ReblockGVCF.gvcf": "gs://broad-gotc-test-storage/ReblockGVCF/input/scientific/NA12878.bge/NA12878.hard-filtered.gvcf.gz",
"ReblockGVCF.gvcf_index": "gs://broad-gotc-test-storage/ReblockGVCF/input/scientific/NA12878.bge/NA12878.hard-filtered.gvcf.gz.tbi",
"ReblockGVCF.calling_interval_list": "gs://gcp-public-data--broad-references/hg38/v0/bge_exome_calling_regions.v1.1.interval_list",
"ReblockGVCF.ref_fasta": "gs://gcp-public-data--broad-references/hg38/v0/Homo_sapiens_assembly38.fasta",
"ReblockGVCF.ref_fasta_index": "gs://gcp-public-data--broad-references/hg38/v0/Homo_sapiens_assembly38.fasta.fai",
"ReblockGVCF.ref_dict": "gs://gcp-public-data--broad-references/hg38/v0/Homo_sapiens_assembly38.dict",
"ReblockGVCF.annotations_to_remove_command": "--format-annotations-to-remove PRI",
"ReblockGVCF.move_filters_to_genotypes": true,
"ReblockGVCF.gvcf_file_extension": ".gvcf.gz"
}
4 changes: 2 additions & 2 deletions ...broad/dna_seq/germline/joint_genotyping/test_inputs/Plumbing/gather_vcfs_high_memory.json
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -9,8 +9,8 @@
"JointGenotyping.snp_recalibration_annotation_values": ["AS_QD", "AS_MQRankSum", "AS_ReadPosRankSum", "AS_FS", "AS_MQ", "AS_SOR"],
"JointGenotyping.indel_recalibration_tranche_values": ["100.0", "99.95", "99.9", "99.5", "99.0", "97.0", "96.0", "95.0", "94.0", "93.5", "93.0", "92.0", "91.0", "90.0"],
"JointGenotyping.indel_recalibration_annotation_values": ["AS_FS", "AS_ReadPosRankSum", "AS_MQRankSum", "AS_QD", "AS_SOR"],
"JointGenotyping.snp_filter_level": 99.7,
"JointGenotyping.indel_filter_level": 95.0,
"JointGenotyping.vqsr_snp_filter_level": 99.7,
"JointGenotyping.vqsr_indel_filter_level": 95.0,
"JointGenotyping.snp_vqsr_downsampleFactor": 1,
"JointGenotyping.hapmap_resource_vcf": "gs://gcp-public-data--broad-references/hg38/v0/hapmap_3.3.hg38.vcf.gz",
"JointGenotyping.omni_resource_vcf": "gs://gcp-public-data--broad-references/hg38/v0/1000G_omni2.5.hg38.vcf.gz",
Expand Down
4 changes: 2 additions & 2 deletions .../broad/dna_seq/germline/joint_genotyping/test_inputs/Plumbing/gather_vcfs_low_memory.json
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -9,8 +9,8 @@
"JointGenotyping.snp_recalibration_annotation_values": ["AS_QD", "AS_MQRankSum", "AS_ReadPosRankSum", "AS_FS", "AS_MQ", "AS_SOR"],
"JointGenotyping.indel_recalibration_tranche_values": ["100.0", "99.95", "99.9", "99.5", "99.0", "97.0", "96.0", "95.0", "94.0", "93.5", "93.0", "92.0", "91.0", "90.0"],
"JointGenotyping.indel_recalibration_annotation_values": ["AS_FS", "AS_ReadPosRankSum", "AS_MQRankSum", "AS_QD", "AS_SOR"],
"JointGenotyping.snp_filter_level": 99.7,
"JointGenotyping.indel_filter_level": 95.0,
"JointGenotyping.vqsr_snp_filter_level": 99.7,
"JointGenotyping.vqsr_indel_filter_level": 95.0,
"JointGenotyping.snp_vqsr_downsampleFactor": 10,
"JointGenotyping.hapmap_resource_vcf": "gs://gcp-public-data--broad-references/hg38/v0/hapmap_3.3.hg38.vcf.gz",
"JointGenotyping.omni_resource_vcf": "gs://gcp-public-data--broad-references/hg38/v0/1000G_omni2.5.hg38.vcf.gz",
Expand Down
4 changes: 2 additions & 2 deletions pipelines/broad/dna_seq/germline/joint_genotyping/test_inputs/Plumbing/gnarly.json
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -9,8 +9,8 @@
"JointGenotyping.snp_recalibration_annotation_values": ["QD", "MQRankSum", "ReadPosRankSum", "FS", "SOR"],
"JointGenotyping.indel_recalibration_tranche_values": ["100.0", "99.95", "99.9", "99.5", "99.0", "97.0", "96.0", "95.0", "94.0", "93.5", "93.0", "92.0", "91.0", "90.0"],
"JointGenotyping.indel_recalibration_annotation_values": ["FS", "ReadPosRankSum", "MQRankSum", "QD", "SOR"],
"JointGenotyping.snp_filter_level": 99.7,
"JointGenotyping.indel_filter_level": 95.0,
"JointGenotyping.vqsr_snp_filter_level": 99.7,
"JointGenotyping.vqsr_indel_filter_level": 95.0,
"JointGenotyping.snp_vqsr_downsampleFactor": 10,
"JointGenotyping.hapmap_resource_vcf": "gs://gcp-public-data--broad-references/hg38/v0/hapmap_3.3.hg38.vcf.gz",
"JointGenotyping.omni_resource_vcf": "gs://gcp-public-data--broad-references/hg38/v0/1000G_omni2.5.hg38.vcf.gz",
Expand Down
4 changes: 2 additions & 2 deletions pipelines/broad/dna_seq/germline/joint_genotyping/test_inputs/Plumbing/plumbing.input.json
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -26,11 +26,11 @@

"JointGenotyping.snp_vqsr_downsampleFactor": 10,
"JointGenotyping.snps_variant_recalibration_threshold": 20000,
"JointGenotyping.snp_filter_level": 99.7,
"JointGenotyping.vqsr_snp_filter_level": 99.7,
"JointGenotyping.snp_recalibration_annotation_values": ["QD", "MQRankSum", "ReadPosRankSum", "FS", "MQ", "SOR", "DP"],
"JointGenotyping.snp_recalibration_tranche_values": ["100.0", "99.95", "99.9", "99.8", "99.6", "99.5", "99.4", "99.3", "99.0", "98.0", "97.0", "90.0" ],

"JointGenotyping.indel_filter_level": 99.0,
"JointGenotyping.vqsr_indel_filter_level": 99.0,
"JointGenotyping.indel_recalibration_annotation_values": ["FS", "ReadPosRankSum", "MQRankSum", "QD", "SOR", "DP"],
"JointGenotyping.indel_recalibration_tranche_values": ["100.0", "99.95", "99.9", "99.5", "99.0", "97.0", "96.0", "95.0", "94.0", "93.5", "93.0", "92.0", "91.0", "90.0"],

Expand Down
4 changes: 2 additions & 2 deletions .../broad/dna_seq/germline/joint_genotyping/test_inputs/Plumbing/shard_vcfs_high_memory.json
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -9,8 +9,8 @@
"JointGenotyping.snp_recalibration_annotation_values": ["AS_QD", "AS_MQRankSum", "AS_ReadPosRankSum", "AS_FS", "AS_MQ", "AS_SOR"],
"JointGenotyping.indel_recalibration_tranche_values": ["100.0", "99.95", "99.9", "99.5", "99.0", "97.0", "96.0", "95.0", "94.0", "93.5", "93.0", "92.0", "91.0", "90.0"],
"JointGenotyping.indel_recalibration_annotation_values": ["AS_FS", "AS_ReadPosRankSum", "AS_MQRankSum", "AS_QD", "AS_SOR"],
"JointGenotyping.snp_filter_level": 99.7,
"JointGenotyping.indel_filter_level": 95.0,
"JointGenotyping.vqsr_snp_filter_level": 99.7,
"JointGenotyping.vqsr_indel_filter_level": 95.0,
"JointGenotyping.snp_vqsr_downsampleFactor": 1,
"JointGenotyping.hapmap_resource_vcf": "gs://gcp-public-data--broad-references/hg38/v0/hapmap_3.3.hg38.vcf.gz",
"JointGenotyping.omni_resource_vcf": "gs://gcp-public-data--broad-references/hg38/v0/1000G_omni2.5.hg38.vcf.gz",
Expand Down
4 changes: 2 additions & 2 deletions ...s/broad/dna_seq/germline/joint_genotyping/test_inputs/Plumbing/shard_vcfs_low_memory.json
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -9,8 +9,8 @@
"JointGenotyping.snp_recalibration_annotation_values": ["AS_QD", "AS_MQRankSum", "AS_ReadPosRankSum", "AS_FS", "AS_MQ", "AS_SOR"],
"JointGenotyping.indel_recalibration_tranche_values": ["100.0", "99.95", "99.9", "99.5", "99.0", "97.0", "96.0", "95.0", "94.0", "93.5", "93.0", "92.0", "91.0", "90.0"],
"JointGenotyping.indel_recalibration_annotation_values": ["AS_FS", "AS_ReadPosRankSum", "AS_MQRankSum", "AS_QD", "AS_SOR"],
"JointGenotyping.snp_filter_level": 99.7,
"JointGenotyping.indel_filter_level": 95.0,
"JointGenotyping.vqsr_snp_filter_level": 99.7,
"JointGenotyping.vqsr_indel_filter_level": 95.0,
"JointGenotyping.snp_vqsr_downsampleFactor": 10,
"JointGenotyping.hapmap_resource_vcf": "gs://gcp-public-data--broad-references/hg38/v0/hapmap_3.3.hg38.vcf.gz",
"JointGenotyping.omni_resource_vcf": "gs://gcp-public-data--broad-references/hg38/v0/1000G_omni2.5.hg38.vcf.gz",
Expand Down
Loading
Loading