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cidc-pipelines

A repo for tracking the versions and composition of CIDC pipelines

v1.0.0 WES whole exome sequencing

Components

name version hash notes
cidc_wes 9b26a3d snakemake github; commit from 6/12/2019
20190709_wesGCP_jason_update.txt ce44437cb14f38aadabc53838ed45fa3 job submission protocol; md5 checksum of text file
wes-ver1-83 1-83 42WmSpB8rSM= google compute image; label fingerprint of the image
reference-disk ??? ??? contains the WES reference data

Environments

name type version notes
pyclone conda ???
optitype conda ??? locally built

Tools

tool version environment notes
bwa 0.7.17-r1188
sentieon 201808.05
sambamba 0.6.8
sequenza 2.1.9999b0 pyclone
PyClone 0.13.1 pyclone
mosdepth 0.2.3
samtools 1.9
vcftools 0.1.16
vep 91.3
pvacseq ???
bedtools v2.28.0
Optitype 1.3.1 optitype
snp-pileup ???
vcf2maf ???
bcftools 1.9

References

reference_key location version source notes
bwa_index_hg38 ./ref_files/hg38/bwa_gdc/GRCh38.d1.vd1.fa
genome_fasta_hg38 ./ref_files/hg38/bwa_gdc/GRCh38.d1.vd1.fa
dbsnp ./ref_files/hg38/snp/Homo_sapiens_assembly38.dbsnp138.vcf
Mills_indels ./ref_files/hg38/snp/Mills_and_1000G_gold_standard.indels.hg38.vcf.gz
G1000_indels ./ref_files/hg38/snp/1000G_phase1.snps.high_confidence.hg38.vcf.gz
CDS_Bed_input ./ref_files/hg38/gencode27.canonical.bed
target_Bed_input ./ref_files/hg38/target_beds/mocha.liftover.hg38.bed
positions_bamtovcf ./ref_files/hg38/target_beds/pos_bamtovcf.bed
positions_SNP92 ./ref_files/hg38/target_beds/pos_filtervcf.bed
vep_data ./ref_files/hg38/vep
vep_plugins ./ref_files/hg38/vep/VEP_plugins
vep_synonyms ./ref_files/hg38/vep/homo_sapiens/91_GRCh38/chr_synonyms.txt
vep_custom_enst ./ref_files/hg38/vep/myc_isoform_overrides_uniprot
vep_fasta ./ref_files/hg38/vep/hg38.canonical.fa
vep_filter ./ref_files/hg38/vep/ExAC_nonTCGA.r0.3.1.sites.vep.vcf.gz
pons ./ref_files/hg38/pons/lung_TCGA_cnv_pad0
pons_target ./ref_files/hg38/pons/MDA_Broad_Miao.target.bed
pons_haplotyper ./ref_files/hg38/pons/TNhaplotyper_PoN.vcf.gz
pons_tnsnv ./ref_files/hg38/pons/TNsnv_PoN.vcf
facets_vcftar ./ref_files/hg38/snp/00-common_all.vcf.gz
gc_file ./ref_files/hg38/clonality/hg38.gc50Base.txt.gz
neoantigen_iedb ./ref_files/hg38/iedb
bwa_index_hg19 ./ref_files/hg19/bwa_indices/hg19/hg19.fa
genome_fasta_hg19 ./path/to/hg19.fasta