Settings¶
This page contains details of the settings used for different tools in the pipeline
Somatic paired variant calling¶
Tool | Step | Argument | Description | Resource |
mutect2 | calling | --panel-of-normals | 1000 Genomes with COSMIC and ClinVar samples removed | /data/CCBR_Pipeliner/Pipelines/XAVIER/resources/hg38/PON/hg38.noCOSMIC_ClinVar.pon.vcf.gz |
--germline-resource | GATK Bundle; reheadered to match genome fasta | /data/CCBR_Pipeliner/Pipelines/XAVIER/resources/hg38/GNOMAD/somatic-hg38-af-only-gnomad.hg38.vcf.gz | ||
-normal | BAM file for paired normal sample | |||
filter | --ob-priors | from GATK LearnReadOrientationModel (uses f1r2 file output during calling) | ||
--contamination-table | from GATK CalculateContamination (uses pileup of tumor AND normal bam) | |||
strelka | calling | --exome | Preset filters for exome data | |
mutect | --normal_panel | 1000 Genomes with COSMIC and ClinVar samples removed | /data/CCBR_Pipeliner/Pipelines/XAVIER/resources/hg38/PON/hg38.noCOSMIC_ClinVar.pon.vcf.gz | |
--cosmic | COSMIC version 82 | /data/CCBR_Pipeliner/db/PipeDB/lib/COSMIC_82_hg38.vcf.gz | ||
--dbsnp | dbSNP version 138 | /fdb/GATK_resource_bundle/hg38bundle/dbsnp_138.hg38.vcf.gz | ||
-rf BadCigar | removes bad cigar strings, similar to https://gatk.broadinstitute.org/hc/en-us/articles/360037430171-GoodCigarReadFilter | |||
vardict | -f 0.05 | Minimum variant allele frequency threshold 0.05 | ||
--nosv | Turn off structural variant calling | |||
-t | Remove duplicated reads | |||
-Q 20 | Reads with quality < 20 are removed | |||
-c 1 | Column of targets BED file with chromosome | |||
-S 2 | Column of targets BED file with start position | |||
-E 3 | Column of targets BED file with end position | |||
var2vcf | -d 10 | Min total depth | ||
-v 6 | Min variant depth | |||
-M | If set, output only candidate somatic | |||
-S | exclude variants that fail filters | |||
filter | --exclude 'STATUS="Germline" | STATUS="LikelyLOH" | STATUS="AFDiff"' | Removes variants with certain flags from vardict; (1) Germline: detected in germline sample (pass all quality parameters); (2) LikelyLOH: detected in germline but either lost in tumor OR 20-80% in germline, but increased to 1-opt_V (95%); (3) AFDiff: detected in tumor (pass quality parameters) and present in germline but didn’t pass quality parameters. | ||
varscan | pileup | -d 100000 -q 15 -Q 15 | samtools mpileup arguments; max depth of 100,000; min mapping quality of 15; min base quality of 15 | |
calling | --strand-filter 0 | Do not ignore variants with >90% support on one strand | ||
--min-var-freq 0.01 | Minimum variant allele frequency threshold 0.01 | |||
--output-vcf 1 | Output in VCF format | |||
--variants 1 | Report only variant (SNP/indel) positions | |||
all | GATK SelectVariants | --exclude-filtered | Removes non-PASS variants | |
--discordance | Remove variants found in supplied file (same as panel-of-normals file) | /data/CCBR_Pipeliner/Pipelines/XAVIER/resources/hg38/PON/hg38.noCOSMIC_ClinVar.pon.vcf.gz |
Somatic tumor-only variant calling¶
Tool | Step | Argument | Description | Resource |
mutect2 | calling | --panel-of-normals | 1000 Genomes with COSMIC and ClinVar samples removed | /data/CCBR_Pipeliner/Pipelines/XAVIER/resources/hg38/PON/hg38.noCOSMIC_ClinVar.pon.vcf.gz |
--germline-resource | GATK Bundle; reheadered to match genome fasta | /data/CCBR_Pipeliner/Pipelines/XAVIER/resources/hg38/GNOMAD/somatic-hg38-af-only-gnomad.hg38.vcf.gz | ||
filter | --ob-priors | from GATK LearnReadOrientationModel (uses f1r2 file output during calling) | ||
--contamination-table | from GATK CalculateContamination (uses pileup of tumor bam) | |||
mutect | calling | --normal_panel | 1000 Genomes with COSMIC and ClinVar samples removed | /data/CCBR_Pipeliner/Pipelines/XAVIER/resources/hg38/PON/hg38.noCOSMIC_ClinVar.pon.vcf.gz |
--cosmic | COSMIC version 82 | /data/CCBR_Pipeliner/Pipelines/XAVIER/resources/hg38/PON/hg38.noCOSMIC_ClinVar.pon.vcf.gz | ||
--dbsnp | dbSNP version 138 | /fdb/GATK_resource_bundle/hg38bundle/dbsnp_138.hg38.vcf.gz | ||
-rf BadCigar | removes bad cigar strings, similar to https://gatk.broadinstitute.org/hc/en-us/articles/360037430171-GoodCigarReadFilter | |||
vardict | -f 0.05 | Minimum variant allele frequency threshold 0.05 | ||
-x 500 | Nucleotides to extend | |||
--nosv | Turn off structural variant calling | |||
-t | Remove duplicated reads | |||
-Q 20 | Reads with map quality < 20 are removed | |||
-c 1 | Column of targets BED file with chromosome | |||
-S 2 | Column of targets BED file with start position | |||
-E 3 | Column of targets BED file with end position | |||
var2vcf | -d 10 | Min total depth | ||
-v 6 | Min variant depth | |||
-S | exclude variants that fail filters | |||
varscan | pileup | -d 100000 -q 15 -Q 15 | samtools mpileup arguments; max depth of 100,000; min mapping quality of 15; min base quality of 15 | |
calling | --strand-filter 0 | Do not ignore variants with >90% support on one strand | ||
--min-var-freq 0.01 | Minimum variant allele frequency threshold 0.01 | |||
--output-vcf 1 | Output in VCF format | |||
--variants 1 | Report only variant (SNP/indel) positions | |||
all | GATK SelectVariants | --exclude-filtered | Removes non-PASS variants | |
--discordance | Remove variants found in supplied file (same as panel-of-normals file) | /data/CCBR_Pipeliner/Pipelines/XAVIER/resources/hg38/PON/hg38.noCOSMIC_ClinVar.pon.vcf.gz |