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varscan repo contains code for Varscan workflow

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varscan

Varscan 2.3, workflow for calling SNVs and CVs Creation of mpileups and calling variants are done with parallel processing varscan outputs

Dependencies

Usage

Cromwell

java -jar cromwell.jar run varscan.wdl --inputs inputs.json

Inputs

Required workflow parameters:

Parameter Value Description
inputTumor File input .bam file for tumor sample
inputNormal File input .bam file for normal sample
inputTumorIndex File input .bai file for tumor sample
inputNormalIndex File input .bai file for normal sample
reference String Reference assembly id, hg19 hg38 or mm10
outputFileNamePrefix String Output file(s) prefix

Optional workflow parameters:

Parameter Value Default Description
bedIntervalsPath String "" Path to a .bed file used for splitting pileup job/limiting analysis to selected regions

Optional task parameters:

Parameter Value Default Description
expandRegions.modules String "hg38-dac-exclusion/1.0" required modules (This is to allow modularized data for bed path)
expandRegions.jobMemory Int 4 Memory for this task in GB
expandRegions.timeout Int 12 Timeout in hours, needed to override imposed limits
getChrCoefficient.memory Int 1 Memory allocated for this job
getChrCoefficient.timeout Int 1 Hours before task timeout
makePileups.samtools String "$SAMTOOLS_ROOT/bin/samtools" path to samtools
makePileups.jobMemory Int 18 memory for this job, in Gb
makePileups.minMemory Int 6 Minimal amount of memory to assign to the task
makePileups.timeout Int 40 Timeout in hours, needed to override imposed limits
runVarscanCNV.pValue Float 0.05 p-value for cnv calling, default is 0.05
runVarscanCNV.jobMemory Int 20 Memory in Gb for this job
runVarscanCNV.minMemory Int 4 A minimum amount of memory allocated to the task, overrides the scaled RAM setting
runVarscanCNV.javaMemory Int 6 Memory in Gb for Java
runVarscanCNV.logFile String "VARSCAN_CNV.log" File for logging Varscan messages
runVarscanCNV.varScan String "$VARSCAN_ROOT/VarScan.jar" path to varscan .jar file
runVarscanCNV.modules String "varscan/2.4.2 java/8" Names and versions of modules
runVarscanCNV.timeout Int 40 Timeout in hours, needed to override imposed limits
getSnvNative.pValue Float 0.05 somatic p-value for SNV calling, default is 0.05
getSnvNative.jobMemory Int 20 Memory in Gb for this job
getSnvNative.minMemory Int 4 A minimum amount of memory allocated to the task, overrides the scaled RAM setting
getSnvNative.javaMemory Int 6 Memory in Gb for Java
getSnvNative.minCoverage Int 8 Minimum coverage in normal and tumor to call variant [8]
getSnvNative.minCoverageNormal Int 8 Minimum coverage in normal to call somatic [8]
getSnvNative.minCoverageTumor Int 6 Minimum coverage in tumor to call somatic [6]
getSnvNative.minVarFreq Float 0.1 Minimum variant frequency to call a heterozygote [0.10]
getSnvNative.minFreqForHom Float 0.75 Minimum frequency to call homozygote [0.75]
getSnvNative.normalPurity Float 1.0 Estimated purity (non-tumor content) of normal sample [1.00]
getSnvNative.tumorPurity Float 1.0 Estimated purity (tumor content) of normal sample [1.00]
getSnvNative.pValueHet Float 0.99 p-value threshold to call a heterozygote [0.99]
getSnvNative.strandFilter Int 0 If set to 1, removes variants with >90% strand bias
getSnvNative.validation Int 0 If set to 1, outputs all compared positions even if non-variant
getSnvNative.outputVcf Int 0 Flag that when set to 1 indicates that we need results in vcf format
getSnvNative.logFile String "VARSCAN_SNV.log" File for logging Varscan messages
getSnvNative.varScan String "$VARSCAN_ROOT/VarScan.jar" path to varscan .jar file
getSnvNative.modules String "varscan/2.4.2 java/8" Names and versions of modules
getSnvNative.timeout Int 40 Timeout in hours, needed to override imposed limits
getSnvVcf.pValue Float 0.05 somatic p-value for SNV calling, default is 0.05
getSnvVcf.jobMemory Int 20 Memory in Gb for this job
getSnvVcf.minMemory Int 4 A minimum amount of memory allocated to the task, overrides the scaled RAM setting
getSnvVcf.javaMemory Int 6 Memory in Gb for Java
getSnvVcf.minCoverage Int 8 Minimum coverage in normal and tumor to call variant [8]
getSnvVcf.minCoverageNormal Int 8 Minimum coverage in normal to call somatic [8]
getSnvVcf.minCoverageTumor Int 6 Minimum coverage in tumor to call somatic [6]
getSnvVcf.minVarFreq Float 0.1 Minimum variant frequency to call a heterozygote [0.10]
getSnvVcf.minFreqForHom Float 0.75 Minimum frequency to call homozygote [0.75]
getSnvVcf.normalPurity Float 1.0 Estimated purity (non-tumor content) of normal sample [1.00]
getSnvVcf.tumorPurity Float 1.0 Estimated purity (tumor content) of normal sample [1.00]
getSnvVcf.pValueHet Float 0.99 p-value threshold to call a heterozygote [0.99]
getSnvVcf.strandFilter Int 0 If set to 1, removes variants with >90% strand bias
getSnvVcf.validation Int 0 If set to 1, outputs all compared positions even if non-variant
getSnvVcf.logFile String "VARSCAN_SNV.log" File for logging Varscan messages
getSnvVcf.varScan String "$VARSCAN_ROOT/VarScan.jar" path to varscan .jar file
getSnvVcf.modules String "varscan/2.4.2 java/8" Names and versions of modules
getSnvVcf.timeout Int 40 Timeout in hours, needed to override imposed limits
mergeCNV.jobMemory Int 6 memory in GB for this job
mergeCNV.timeout Int 10 Timeout in hours, needed to override imposed limits
mergeSNP.jobMemory Int 6 memory in GB for this job
mergeSNP.timeout Int 10 Timeout in hours, needed to override imposed limits
mergeIND.jobMemory Int 6 memory in GB for this job
mergeIND.timeout Int 10 Timeout in hours, needed to override imposed limits
mergeSNPvcf.jobMemory Int 12 memory in GB for this job
mergeSNPvcf.javaMemory Int 8 memory in GB for java VM
mergeSNPvcf.timeout Int 10 Timeout in hours, needed to override imposed limits
mergeINDvcf.jobMemory Int 12 memory in GB for this job
mergeINDvcf.javaMemory Int 8 memory in GB for java VM
mergeINDvcf.timeout Int 10 Timeout in hours, needed to override imposed limits
smoothData.varScan String "$VARSCAN_ROOT/VarScan.jar" Path to VarScan jar file
smoothData.modules String "varscan/2.4.2 java/8 rstats/3.6" Modules for this job
smoothData.min_coverage Int 20 Fine-tuning parameter for VarScan
smoothData.max_homdel_coverage Int 5 Max coverage form homozygous deletion, default is 5
smoothData.min_tumor_coverage Int 10 Min coverage in tumor sample, default is 10
smoothData.del_threshold Float 0.25 Fine-tuning parameter for VarScan
smoothData.amp_threshold Float 0.25 Amplification threshold to report, default is 0.25
smoothData.min_region_size Int 10 Fine-tuning parameter for VarScan
smoothData.recenter_up Int 0 Fine-tuning parameter for VarScan
smoothData.recenter_down Int 0 Fine-tuning parameter for VarScan
smoothData.jobMemory Int 16 Memory in Gb for this job
smoothData.javaMemory Int 6 Memory in Gb for Java

Outputs

Output Type Description Labels
resultCnvFile File? file with CNV calls, smoothed vidarr_label: resultCnvFile
resultSnpFile File file with SNPs, native varscan format vidarr_label: resultSnpFile
resultIndelFile File file with Indel calls, native varscan format vidarr_label: resultIndelFile
resultSnpVcfFile File file with SNPs, vcf format vidarr_label: resultSnpVcfFile
resultIndelVcfFile File file with Indels, vcf format vidarr_label: resultIndelVcfFile

Commands

This section lists command(s) run by varscan workflow

Produce a scaling coefficient for allocating RAM

   CHROM=$(echo ~{region} | sed 's/:.*//')
   grep -w SN:$CHROM ~{refDict} | cut -f 3 | sed 's/.*://' | awk '{print int(($1/~{largestChrom} + 0.1) * 10)/10}'

Preprocessing

bed file re-format to be used with scattered pileup creation. Note that it should be a resonable ( <100 perhaps? ) intervals so that we do not end up with a million jobs running. Use wisely, as it may result in grabbing a lot of compute nodes.

  In this embedded script we reformat bed lines into varscan-friendly intervals
 
  import os
  if os.path.exists("~{bedPath}"):
     with open("~{bedPath}") as f:
         for line in f:
            line = line.rstrip()
            tmp = line.split("\t")
            r = " " + tmp[0] + ":" + tmp[1] + "-" + tmp[2]
            print(r)
     f.close()

Run samtools mpileup

  samtools mpileup -q 1 -r REGION -f REF_FASTA INPUT_NORMAL INPUT_TUMOR | awk -F "\t" '$4 > 0 && $7 > 0' | gzip -c > normtumor_sorted.pileup.gz

Remove mitochondrial chromosome:

  head -n 1 ~{filePaths[0]} > "~{outputFile}.~{outputExtension}"
  cat ~{sep=' ' filePaths} | sort -V -k 1,2 | grep -v ^chrom | grep -v ^chrM >> "~{outputFile}.~{outputExtension}"
  cat ~{sep=' ' filePaths} | awk '{if($1 == "chrM"){print $0}}' | sort -V -k 1,2 >> "~{outputFile}.~{outputExtension}"
  if [ ! -s ~{outputFile}.~{outputExtension} ] ; then
   rm ~{outputFile}.~{outputExtension}
  fi

Sort vcf using sequence dictionary

  java -Xmx[MEMORY]G -jar picard.jar SortVcf I=INPUT_VCFS SD=SEQ_DICTIONARY O=OUTPUT_FILE.SUFFIX.vcf

SNP/Indel Calling:

   See the full source code in .wdl, here we run this command:
 
   zcat INPUT_PILEUP | java -Xmx[MEMORY]G -jar varscan somatic -mpileup 1 
      --somatic-p-value P_VALUE
 
      Optional parameters:
 
     --min-coverage-normal MIN_COVERAGE_NORMAL
     --min-coverage-tumor  MIN_COVERAGE_TUMOR
     --min-var-freq MIN_VAR_FREQUENCY
     --min-freq-for-hom MIN_FREQUENCY_FOR_HOM
     --normal-purity NORMAL_PURITY
     --tumor-purity TUMOR_PURIY
     --p-value P_VALUE_HET
     --strand-filter 1
     --validation 1
     --output-vcf 1
     
     Settings for output format:
 
     --output-snp SAMPLE_ID.snp.vcf --output-indel SAMPLE_ID.indel.vcf
   
     or:
 
     --output-snp SAMPLE_ID.snp --output-indel SAMPLE_ID.indel

Find minimum coverage threshold for CV analysis:

 
 A python code configures and runs this command: 
 
 zcat ~{inputPileup} | java -Xmx~{javaMemory}G -jar " + varscan + " copynumber --output-file ~{sampleID} -mpileup 1 --p-value ~{pValue}"
 
 Varscan reports if the coverage threshold was sufficient for the analysis. We use this coverage setting in the next step

Run copy number change analysis:

 
 A python code configures and runs this command:
  
 java -Xmx[MEMORY]G -jar varscan copyCaller CV_FILE 
                    --output-file SAMPLE_ID.copynumber.filtered
                    --min-coverage MIN_COVERAGE # Value found in the previous step
 
                     Optional parameters:
 
                    --min-tumor-coverage  MIN_TUMOR_COVERAGE
                    --max-homdel-coverage MAX_HOMDEL_COVERAGE
                    --del-threshold   DEL_THRESHOLD
                    --amp-threshold   AMP_THRESHOLD
                    --min-region-size MIN_REGION_SIZE
                    --recenter-up     RECENTER_UP
                    --recenter-down   RECENTER_DOWN

Support

For support, please file an issue on the Github project or send an email to gsi@oicr.on.ca .

Generated with generate-markdown-readme (https://github.com/oicr-gsi/gsi-wdl-tools/)

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varscan repo contains code for Varscan workflow

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workflow variant-calling snv cnv cromwell varscan

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