A repo for tracking the versions and composition of CIDC pipelines
| 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 |
| name | type | version | notes |
|---|---|---|---|
| pyclone | conda | ??? | |
| optitype | conda | ??? | locally built |
| 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 |
| 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 |