mutect2

Somatic short variant analysis.

Overview

Dependencies

• samtools 1.9

Usage

Cromwell

java -jar cromwell.jar run mutect2.wdl --inputs inputs.json

Inputs

Required workflow parameters:

Parameter	Value	Description
tumorBam	File	Input tumor file (bam or sam).
tumorBai	File	Index for tumorBam
reference	String	the reference genome for input sample
gatk	String	gatk version to be used
outputFileNamePrefix	String	prefix of output file

Optional workflow parameters:

Parameter	Value	Default	Description
normalBam	File?	None	Input normal file (bam or sam).
normalBai	File?	None	Index for noramlBam
intervalFile	String?	None	One or more genomic intervals over which to operate
intervalsToParallelizeBy	String?	None	Comma separated list of intervals to split by (e.g. chr1,chr2,chr3+chr4)
pon	File?	None	panel of normal
ponIdx	File?	None	index of pon

Optional task parameters:

Parameter	Value	Default	Description
splitStringToArray.lineSeparator	String	","	Interval group separator - these are the intervals to split by.
splitStringToArray.memory	Int	1	Memory allocated to job (in GB)
splitStringToArray.timeout	Int	1	Maximum amount of time (in hours) the task can run for.
getChrCoefficient.memory	Int	1	Memory allocated for this job
getChrCoefficient.timeout	Int	1	Hours before task timeout
runMutect2.mutectTag	String	"mutect2"	version tag for mutect
runMutect2.mutect2ExtraArgs	String?	None	placehoulder for extra arguments
runMutect2.threads	Int	4	Requested CPU threads
runMutect2.memory	Int	32	Memory allocated to job (in GB).
runMutect2.minMemory	Int	6	A minimum amount of memory allocated to the task, overrides the scaled RAM setting
runMutect2.timeout	Int	24	Maximum amount of time (in hours) the task can run for.
mergeVCFs.memory	Int	4	Memory allocated for job
mergeVCFs.timeout	Int	12	Hours before task timeout
mergeStats.memory	Int	4	Memory allocated for job
mergeStats.timeout	Int	5	Hours before task timeout
filter.filterExtraArgs	String?	None	placehoulder for extra arguments
filter.memory	Int	16	Memory allocated for job
filter.timeout	Int	12	Hours before task timeout

Outputs

Output	Type	Description	Labels
filteredVcfFile	File	the filtered vcf file	vidarr_label: filteredVcfFile
filteredVcfIndex	File	Index of filtered vcf file	vidarr_label: filteredVcfIndex
mergedUnfilteredStats	File	Stats for merged unfiltered files	vidarr_label: mergedUnfilteredStats
filteringStats	File	Stats for filtering process	vidarr_label: filteringStats

Commands

This section lists command(s) run by mutect2 workflow

• Running mutect2

Mutect requires alignment files (.bam) as an input. Also, various other resources are needed. The results produced by the workflow are variant calls, provisioned as a .vcf file.

Split interval string by comma

    echo "~{intervalsToParallelizeBy}" | tr '~{lineSeparator}' '\n'

Getting Chromosome Scaling Coefficient

     CHROM=$(echo ~{region} | sed 's/:.*//')
     LARGEST=$(grep SN:chr ~{refDict} | cut -f 3 | sed 's/LN://' | sort -n | tail -n 1)
     grep -w SN:$CHROM ~{refDict} | cut -f 3 | sed 's/.*://' | awk -v largest_chr=$LARGEST '{print int(($1/largest_chr + 0.1) * 10)/10}'

Mutect2 (GATK)

     set -euo pipefail
 
     gatk --java-options "-Xmx1g" GetSampleName -R ~{refFasta} -I ~{tumorBam} -O tumor_name.txt -encode
     tumor_command_line="-I ~{tumorBam} -tumor `cat tumor_name.txt`"
 
     cp ~{refFai} .
     cp ~{refDict} .
 
     if [ -f "~{normalBam}" ]; then
       gatk --java-options "-Xmx1g" GetSampleName -R ~{refFasta} -I ~{normalBam} -O normal_name.txt -encode
       normal_command_line="-I ~{normalBam} -normal `cat normal_name.txt`"
     else
       normal_command_line=""
     fi
 
     if [ -f "~{intervalFile}" ]; then
       if ~{intervalsProvided} ; then
         intervals_command_line="-L ~{sep=" -L " intervals} -L ~{intervalFile} -isr INTERSECTION"
       else
         intervals_command_line="-L ~{intervalFile}"
       fi
     else
       if ~{intervalsProvided} ; then
         intervals_command_line="-L ~{sep=" -L " intervals} "
       fi
     fi
 
     if [[ ! -z "~{gnomad}" ]] ; then
       germline_resource_line="--germline-resource ~{gnomad}"
     else 
       germline_resource_line=""
     fi
 
     gatk --java-options "-Xmx~{memory-8}g" Mutect2 \
     -R ~{refFasta} \
     $tumor_command_line \
     $normal_command_line \
     $germline_resource_line \
     ~{"-pon " + pon} \
     $intervals_command_line \
     -O "~{outputVcf}" \
     ~{mutect2ExtraArgs}

MergeVcfs (GATK)

   set -euo pipefail
 
   gatk --java-options "-Xmx~{memory-3}g" MergeVcfs \
   -I ~{sep=" -I " vcfs} \
   -O ~{outputName}

MergeMutectStats (GATK)

   set -euo pipefail
 
   gatk --java-options "-Xmx~{memory-3}g" MergeMutectStats \
   -stats ~{sep=" -stats " stats} \
   -O ~{outputStats}

FilterMutectCalls (GATK)

   set -euo pipefail

   cp ~{refFai} .
   cp ~{refDict} .
 
   gatk --java-options "-Xmx~{memory-4}g" FilterMutectCalls \
   -V ~{unfilteredVcf} \
   -R ~{refFasta} \
   -O ~{filteredVcfName} \
   ~{"-stats " + mutectStats} \
   --filtering-stats ~{filteredVcfName}.stats \
   ~{filterExtraArgs}
 
   bgzip -c ~{filteredVcfName} > ~{filteredVcfName}.gz
   bgzip -c ~{unfilteredVcf} > ~{unfilteredVcfName}.gz
 
   gatk --java-options "-Xmx~{memory-5}g" IndexFeatureFile -I ~{filteredVcfName}.gz
   gatk --java-options "-Xmx~{memory-5}g" IndexFeatureFile -I ~{unfilteredVcfName}.gz

Support

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

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