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
`gnomad`	File?	None	Genome Aggregation Database
`gnomadIdx`	File?	None	Index of gnomad

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.
`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.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
`filteredVcfFile`	File	the filtered vcf file
`filteredVcfIndex`	File	Index of filtered vcf file
`mergedUnfilteredStats`	File	Stats for merged unfiltered files
`filteringStats`	File	Stats for filtering process

Commands

This section lists command(s) run by mutect2 workflow

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

    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

    gatk --java-options "-Xmx~{memory-8}g" Mutect2 \
    -R ~{refFasta} \
    $tumor_command_line \
    $normal_command_line \
    ~{"--germline-resource " + gnomad} \
    ~{"-pon " + pon} \
    $intervals_command_line \
    -O "~{outputVcf}" \
    ~{mutect2ExtraArgs}
  ```

  set -euo pipefail

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

    set -euo pipefail

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

  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 .

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

oicr-gsi/mutect2