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oicr-gsi / mutect2Consensus

The Mutect2Consensus workflow will process umiConsensus outputs for the tumour data through mutect2 in tumour only mode to call variants then use information from the matched normal to identify likely germline variants.

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mutect2Consensus

The Mutect2Consensus workflow will process umiConsensus outputs for the tumour data through mutect2 in tumour only mode to call variants then use information from the matched normal to identify likely germline variants.

Overview

Dependencies

Usage

Cromwell

java -jar cromwell.jar run mutect2Consensus.wdl --inputs inputs.json

Inputs

Required workflow parameters:

Parameter Value Description
tumorInputGroup InputGroup partitioned bam files from umiConsensus outputs for tumor sample
normalInputGroup InputGroup partitioned bam files from umiConsensus outputs for normal sample
intervalFile String interval file to subset variant calls
inputIntervalsToParalellizeBy String intervals for parallelization
tumorName String Name of the tumor sample
normalName String name of the normal sample
reference String reference version
gatk String gatk version to be used
combineVariants.workflows Array[String] array of ids of producer workflows
matchedCombineVariants.workflows Array[String] array of ids of producer workflows

Optional workflow parameters:

Parameter Value Default Description

Optional task parameters:

Parameter Value Default Description
mutect2.filter_timeout Int 12 Hours before task timeout
mutect2.filter_memory Int 16 Memory allocated for job
mutect2.filter_filterExtraArgs String? None placehoulder for extra arguments
mutect2.mergeStats_timeout Int 5 Hours before task timeout
mutect2.mergeStats_memory Int 4 Memory allocated for job
mutect2.mergeVCFs_timeout Int 12 Hours before task timeout
mutect2.mergeVCFs_memory Int 4 Memory allocated for job
mutect2.runMutect2_timeout Int 24 Maximum amount of time (in hours) the task can run for.
mutect2.runMutect2_memory Int 32 Memory allocated to job (in GB).
mutect2.runMutect2_threads Int 4 Requested CPU threads
mutect2.runMutect2_mutect2ExtraArgs String? None placehoulder for extra arguments
mutect2.runMutect2_mutectTag String "mutect2" version tag for mutect
mutect2.splitStringToArray_timeout Int 1 Maximum amount of time (in hours) the task can run for.
mutect2.splitStringToArray_memory Int 1 Memory allocated to job (in GB)
mutect2.splitStringToArray_lineSeparator String "," Interval group separator - these are the intervals to split by.
mutect2.normalBam File? None Input normal file (bam or sam).
mutect2.normalBai File? None Index for noramlBam
mutect2.pon File? None panel of normal
mutect2.ponIdx File? None index of pon
mutect2.gnomad File? None Genome Aggregation Database
mutect2.gnomadIdx File? None Index of gnomad
combineVariants.jobMemory Int 24 memory allocated to preprocessing, in GB
combineVariants.timeout Int 20 timeout in hours
combineVariants.threads Int 8 number of cpu threads to be used
annotation.modules String "samtools/1.9 bcftools/1.9 htslib/1.9 tabix/1.9" module for running preprocessing
annotation.jobMemory Int 24 memory allocated to preprocessing, in GB
annotation.timeout Int 20 timeout in hours
annotation.threads Int 8 number of cpu threads to be used
variantEffectPredictor.mergeVcfs_timeout Int 24 Maximum amount of time (in hours) the task can run for.
variantEffectPredictor.mergeVcfs_threads Int 4 Requested CPU threads.
variantEffectPredictor.mergeVcfs_overhead Int 6 Java overhead memory (in GB). jobMemory - overhead == java Xmx/heap memory.
variantEffectPredictor.mergeVcfs_jobMemory Int 24 Memory allocated to job (in GB).
variantEffectPredictor.mergeVcfs_extraArgs String? None Additional arguments to be passed directly to the command.
variantEffectPredictor.mergeVcfs_modules String "gatk/4.1.7.0" Required environment modules.
variantEffectPredictor.mergeMafs_timeout Int 24 Maximum amount of time (in hours) the task can run for.
variantEffectPredictor.mergeMafs_threads Int 4 Requested CPU threads.
variantEffectPredictor.mergeMafs_jobMemory Int 24 Memory allocated to job (in GB).
variantEffectPredictor.mergeMafs_modules String "tabix/0.2.6" Required environment modules
variantEffectPredictor.vcf2maf_timeout Int 48 Hours before task timeout
variantEffectPredictor.vcf2maf_threads Int 4 Requested CPU threads
variantEffectPredictor.vcf2maf_jobMemory Int 32 Memory allocated for this job (GB)
variantEffectPredictor.vcf2maf_bufferSize Int 200 The buffer size
variantEffectPredictor.vcf2maf_minHomVaf Float 0.7 The minimum vaf for homozygous calls
variantEffectPredictor.vcf2maf_vepStats Boolean true If vepStats is true, remove flag '--no_stats' from vep. If vepStats is false, running vep with flag '--no_stats'
variantEffectPredictor.vcf2maf_basename String basename("~{vcfFile}",".vcf.gz") Base name
variantEffectPredictor.tumorOnlyAlign_timeout Int 6 Hours before task timeout
variantEffectPredictor.tumorOnlyAlign_threads Int 4 Requested CPU threads
variantEffectPredictor.tumorOnlyAlign_jobMemory Int 32 Memory allocated for this job (GB)
variantEffectPredictor.tumorOnlyAlign_modules String "bcftools/1.9 tabix/0.2.6" Required environment modules
variantEffectPredictor.tumorOnlyAlign_basename String basename("~{vcfFile}",".vcf.gz") Base name
variantEffectPredictor.vep_timeout Int 16 Hours before task timeout
variantEffectPredictor.vep_threads Int 4 Requested CPU threads
variantEffectPredictor.vep_jobMemory Int 32 Memory allocated for this job (GB)
variantEffectPredictor.vep_vepStats Boolean true If vepStats is true, remove flag '--no_stats' from vep. If vepStats is false, running vep with flag '--no_stats'
variantEffectPredictor.vep_addParam String? None Additional vep parameters
variantEffectPredictor.vep_basename String basename("~{vcfFile}",".vcf.gz") Base name
variantEffectPredictor.subsetVcf_timeout Int 6 Maximum amount of time (in hours) the task can run for.
variantEffectPredictor.subsetVcf_threads Int 4 Requested CPU threads.
variantEffectPredictor.subsetVcf_jobMemory Int 32 Memory allocated to job (in GB).
variantEffectPredictor.subsetVcf_modules String "bcftools/1.9" Required environment modules
variantEffectPredictor.subsetVcf_basename String basename("~{vcfFile}",".vcf.gz") Base name
variantEffectPredictor.chromosomeArray_timeout Int 1 Maximum amount of time (in hours) the task can run for.
variantEffectPredictor.chromosomeArray_threads Int 4 Requested CPU threads.
variantEffectPredictor.chromosomeArray_jobMemory Int 1 Memory allocated to job (in GB).
variantEffectPredictor.getSampleNames_timeout Int 1 Hours before task timeout
variantEffectPredictor.getSampleNames_threads Int 4 Requested CPU threads
variantEffectPredictor.getSampleNames_jobMemory Int 1 Memory allocated for this job (GB)
variantEffectPredictor.targetBedTask_timeout Int 6 Hours before task timeout
variantEffectPredictor.targetBedTask_threads Int 4 Requested CPU threads
variantEffectPredictor.targetBedTask_jobMemory Int 32 Memory allocated for this job (GB)
variantEffectPredictor.targetBedTask_modules String "bedtools/2.27 tabix/0.2.6" Required environment modules
variantEffectPredictor.targetBedTask_basename String basename("~{vcfFile}",".vcf.gz") Base name
variantEffectPredictor.normalName String? None Name of the normal sample
filterMaf.freqList String "$MAF_FILTERING_ROOT/TGL.frequency.20210609.annot.txt" frequency list used in maf annotation
filterMaf.genesToKeep String "$MAF_FILTERING_ROOT/genes_to_keep.txt" gene list in maf filtering
filterMaf.modules String "python/3.9 pandas/1.4.2 maf-filtering/2023-10-06" module for running preprocessing
filterMaf.jobMemory Int 8 memory allocated to preprocessing, in GB
filterMaf.timeout Int 1 timeout in hours
filterMaf.threads Int 1 number of cpu threads to be used
matchedMutect2.filter_timeout Int 12 Hours before task timeout
matchedMutect2.filter_memory Int 16 Memory allocated for job
matchedMutect2.filter_filterExtraArgs String? None placehoulder for extra arguments
matchedMutect2.mergeStats_timeout Int 5 Hours before task timeout
matchedMutect2.mergeStats_memory Int 4 Memory allocated for job
matchedMutect2.mergeVCFs_timeout Int 12 Hours before task timeout
matchedMutect2.mergeVCFs_memory Int 4 Memory allocated for job
matchedMutect2.runMutect2_timeout Int 24 Maximum amount of time (in hours) the task can run for.
matchedMutect2.runMutect2_memory Int 32 Memory allocated to job (in GB).
matchedMutect2.runMutect2_threads Int 4 Requested CPU threads
matchedMutect2.runMutect2_mutect2ExtraArgs String? None placehoulder for extra arguments
matchedMutect2.runMutect2_mutectTag String "mutect2" version tag for mutect
matchedMutect2.splitStringToArray_timeout Int 1 Maximum amount of time (in hours) the task can run for.
matchedMutect2.splitStringToArray_memory Int 1 Memory allocated to job (in GB)
matchedMutect2.splitStringToArray_lineSeparator String "," Interval group separator - these are the intervals to split by.
matchedMutect2.pon File? None panel of normal
matchedMutect2.ponIdx File? None index of pon
matchedMutect2.gnomad File? None Genome Aggregation Database
matchedMutect2.gnomadIdx File? None Index of gnomad
matchedCombineVariants.jobMemory Int 24 memory allocated to preprocessing, in GB
matchedCombineVariants.timeout Int 20 timeout in hours
matchedCombineVariants.threads Int 8 number of cpu threads to be used
matchedAnnotation.modules String "samtools/1.9 bcftools/1.9 htslib/1.9 tabix/1.9" module for running preprocessing
matchedAnnotation.jobMemory Int 24 memory allocated to preprocessing, in GB
matchedAnnotation.timeout Int 20 timeout in hours
matchedAnnotation.threads Int 8 number of cpu threads to be used
matchedVep.mergeVcfs_timeout Int 24 Maximum amount of time (in hours) the task can run for.
matchedVep.mergeVcfs_threads Int 4 Requested CPU threads.
matchedVep.mergeVcfs_overhead Int 6 Java overhead memory (in GB). jobMemory - overhead == java Xmx/heap memory.
matchedVep.mergeVcfs_jobMemory Int 24 Memory allocated to job (in GB).
matchedVep.mergeVcfs_extraArgs String? None Additional arguments to be passed directly to the command.
matchedVep.mergeVcfs_modules String "gatk/4.1.7.0" Required environment modules.
matchedVep.mergeMafs_timeout Int 24 Maximum amount of time (in hours) the task can run for.
matchedVep.mergeMafs_threads Int 4 Requested CPU threads.
matchedVep.mergeMafs_jobMemory Int 24 Memory allocated to job (in GB).
matchedVep.mergeMafs_modules String "tabix/0.2.6" Required environment modules
matchedVep.vcf2maf_timeout Int 48 Hours before task timeout
matchedVep.vcf2maf_threads Int 4 Requested CPU threads
matchedVep.vcf2maf_jobMemory Int 32 Memory allocated for this job (GB)
matchedVep.vcf2maf_bufferSize Int 200 The buffer size
matchedVep.vcf2maf_minHomVaf Float 0.7 The minimum vaf for homozygous calls
matchedVep.vcf2maf_vepStats Boolean true If vepStats is true, remove flag '--no_stats' from vep. If vepStats is false, running vep with flag '--no_stats'
matchedVep.vcf2maf_basename String basename("~{vcfFile}",".vcf.gz") Base name
matchedVep.tumorOnlyAlign_timeout Int 6 Hours before task timeout
matchedVep.tumorOnlyAlign_threads Int 4 Requested CPU threads
matchedVep.tumorOnlyAlign_jobMemory Int 32 Memory allocated for this job (GB)
matchedVep.tumorOnlyAlign_modules String "bcftools/1.9 tabix/0.2.6" Required environment modules
matchedVep.tumorOnlyAlign_basename String basename("~{vcfFile}",".vcf.gz") Base name
matchedVep.vep_timeout Int 16 Hours before task timeout
matchedVep.vep_threads Int 4 Requested CPU threads
matchedVep.vep_jobMemory Int 32 Memory allocated for this job (GB)
matchedVep.vep_vepStats Boolean true If vepStats is true, remove flag '--no_stats' from vep. If vepStats is false, running vep with flag '--no_stats'
matchedVep.vep_addParam String? None Additional vep parameters
matchedVep.vep_basename String basename("~{vcfFile}",".vcf.gz") Base name
matchedVep.subsetVcf_timeout Int 6 Maximum amount of time (in hours) the task can run for.
matchedVep.subsetVcf_threads Int 4 Requested CPU threads.
matchedVep.subsetVcf_jobMemory Int 32 Memory allocated to job (in GB).
matchedVep.subsetVcf_modules String "bcftools/1.9" Required environment modules
matchedVep.subsetVcf_basename String basename("~{vcfFile}",".vcf.gz") Base name
matchedVep.chromosomeArray_timeout Int 1 Maximum amount of time (in hours) the task can run for.
matchedVep.chromosomeArray_threads Int 4 Requested CPU threads.
matchedVep.chromosomeArray_jobMemory Int 1 Memory allocated to job (in GB).
matchedVep.getSampleNames_timeout Int 1 Hours before task timeout
matchedVep.getSampleNames_threads Int 4 Requested CPU threads
matchedVep.getSampleNames_jobMemory Int 1 Memory allocated for this job (GB)
matchedVep.targetBedTask_timeout Int 6 Hours before task timeout
matchedVep.targetBedTask_threads Int 4 Requested CPU threads
matchedVep.targetBedTask_jobMemory Int 32 Memory allocated for this job (GB)
matchedVep.targetBedTask_modules String "bedtools/2.27 tabix/0.2.6" Required environment modules
matchedVep.targetBedTask_basename String basename("~{vcfFile}",".vcf.gz") Base name
matchedVep.targetBed String? None Target bed file
matchedFilterMaf.mafNormalFile File? None input file for normal sample
matchedFilterMaf.freqList String "$MAF_FILTERING_ROOT/TGL.frequency.20210609.annot.txt" frequency list used in maf annotation
matchedFilterMaf.genesToKeep String "$MAF_FILTERING_ROOT/genes_to_keep.txt" gene list in maf filtering
matchedFilterMaf.modules String "python/3.9 pandas/1.4.2 maf-filtering/2023-10-06" module for running preprocessing
matchedFilterMaf.jobMemory Int 8 memory allocated to preprocessing, in GB
matchedFilterMaf.timeout Int 1 timeout in hours
matchedFilterMaf.threads Int 1 number of cpu threads to be used

Outputs

Output Type Description
tumorVepVcf File {'description': 'vep vcf for tumor sample', 'vidarr_label': 'tumorVepVcf'}
tumorVepVcfIndex File {'description': 'vep vcf index for tumor sample', 'vidarr_label': 'tumorVepVcfIndex'}
normalVepVcf File {'description': 'vep vcf for normal sample', 'vidarr_label': 'normalVepVcf'}
normalVepVcfIndex File {'description': 'vep vcf index for normal sample', 'vidarr_label': 'normalVepVcfIndex'}
matchedVepVcf File {'description': 'vep vcf for matched samples', 'vidarr_label': 'matchedVepVcf'}
matchedVepVcfIndex File {'description': 'vep vcf index for matched samples', 'vidarr_label': 'matchedVepVcfIndex'}
filteredMaf File? {'description': 'maf file after filtering', 'vidarr_label': 'filterredMaf'}
matchedFilteredMaf File? {'description': 'maf file after filtering for matched maf(maf file of matched tumor/normal version)', 'vidarr_label': 'matchedFilterredMaf'}

Commands

This section lists command(s) run by mutect2Consensus workflow

  • Running mutect2Consensus
   python3<<CODE
   import subprocess
   import sys
   inputStrings = []
   v = "~{sep=' ' inputVcfs}"
   vcfFiles = v.split()
   w = "~{sep=' ' workflows}"
   workflowIds = w.split()
   priority = "~{priority}"
   
   if len(vcfFiles) != len(workflowIds):
       print("The arrays with input files and their respective workflow names are not of equal size!")
   else:
       for f in range(0, len(vcfFiles)):
           inputStrings.append("--variant:" + workflowIds[f] + " " + vcfFiles[f])
 
   javaMemory = ~{jobMemory} - 6 
   gatkCommand  = "$JAVA_ROOT/bin/java -Xmx" + str(javaMemory) + "G -jar $GATK_ROOT/GenomeAnalysisTK.jar "
   gatkCommand += "-T CombineVariants "
   gatkCommand += " ".join(inputStrings)
   gatkCommand += " -R ~{referenceFasta} "
   gatkCommand += "-o ~{outputPrefix}_combined.vcf.gz "
   gatkCommand += "-genotypeMergeOptions PRIORITIZE "
   gatkCommand += "-priority " + priority
   gatkCommand += " 2>&1"
 
   result_output = subprocess.run(gatkCommand, shell=True)
   sys.exit(result_output.returncode)
   CODE


  bcftools annotate -a ~{uniqueVcf} \
 -c FMT/AD,FMT/DP ~{mergedVcf} -Oz \
 -o "~{outputPrefix}.merged.vcf.gz"

 tabix -p vcf "~{outputPrefix}.merged.vcf.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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About

The Mutect2Consensus workflow will process umiConsensus outputs for the tumour data through mutect2 in tumour only mode to call variants then use information from the matched normal to identify likely germline variants.

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