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

• gatk 3.6-0
• python 3.9
• vep 105.0
• gatk 4.1.6.0
• tabix 0.2.6
• vcf2maf 1.6
• pandas 1.4.2

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
filterMafFile	Boolean	whether filter the maf file
combineVariants.workflows	Array[String]	array of ids of producer workflows
somaticCombineVariants.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.targetBed	String?	None	Target bed file
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.modules	String	"python/3.9 pandas/1.4.2 maf-filtering/2024-07-10"	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
somaticMutect2.filter_timeout	Int	12	Hours before task timeout
somaticMutect2.filter_memory	Int	16	Memory allocated for job
somaticMutect2.filter_filterExtraArgs	String?	None	placehoulder for extra arguments
somaticMutect2.mergeStats_timeout	Int	5	Hours before task timeout
somaticMutect2.mergeStats_memory	Int	4	Memory allocated for job
somaticMutect2.mergeVCFs_timeout	Int	12	Hours before task timeout
somaticMutect2.mergeVCFs_memory	Int	4	Memory allocated for job
somaticMutect2.runMutect2_timeout	Int	24	Maximum amount of time (in hours) the task can run for.
somaticMutect2.runMutect2_memory	Int	32	Memory allocated to job (in GB).
somaticMutect2.runMutect2_threads	Int	4	Requested CPU threads
somaticMutect2.runMutect2_mutect2ExtraArgs	String?	None	placehoulder for extra arguments
somaticMutect2.runMutect2_mutectTag	String	"mutect2"	version tag for mutect
somaticMutect2.splitStringToArray_timeout	Int	1	Maximum amount of time (in hours) the task can run for.
somaticMutect2.splitStringToArray_memory	Int	1	Memory allocated to job (in GB)
somaticMutect2.splitStringToArray_lineSeparator	String	","	Interval group separator - these are the intervals to split by.
somaticMutect2.pon	File?	None	panel of normal
somaticMutect2.ponIdx	File?	None	index of pon
somaticMutect2.gnomad	File?	None	Genome Aggregation Database
somaticMutect2.gnomadIdx	File?	None	Index of gnomad
somaticCombineVariants.jobMemory	Int	24	memory allocated to preprocessing, in GB
somaticCombineVariants.timeout	Int	20	timeout in hours
somaticCombineVariants.threads	Int	8	number of cpu threads to be used
somaticAnnotation.modules	String	"samtools/1.9 bcftools/1.9 htslib/1.9 tabix/1.9"	module for running preprocessing
somaticAnnotation.jobMemory	Int	24	memory allocated to preprocessing, in GB
somaticAnnotation.timeout	Int	20	timeout in hours
somaticAnnotation.threads	Int	8	number of cpu threads to be used
somaticVep.mergeVcfs_timeout	Int	24	Maximum amount of time (in hours) the task can run for.
somaticVep.mergeVcfs_threads	Int	4	Requested CPU threads.
somaticVep.mergeVcfs_overhead	Int	6	Java overhead memory (in GB). jobMemory - overhead == java Xmx/heap memory.
somaticVep.mergeVcfs_jobMemory	Int	24	Memory allocated to job (in GB).
somaticVep.mergeVcfs_extraArgs	String?	None	Additional arguments to be passed directly to the command.
somaticVep.mergeVcfs_modules	String	"gatk/4.1.7.0"	Required environment modules.
somaticVep.mergeMafs_timeout	Int	24	Maximum amount of time (in hours) the task can run for.
somaticVep.mergeMafs_threads	Int	4	Requested CPU threads.
somaticVep.mergeMafs_jobMemory	Int	24	Memory allocated to job (in GB).
somaticVep.mergeMafs_modules	String	"tabix/0.2.6"	Required environment modules
somaticVep.vcf2maf_timeout	Int	48	Hours before task timeout
somaticVep.vcf2maf_threads	Int	4	Requested CPU threads
somaticVep.vcf2maf_jobMemory	Int	32	Memory allocated for this job (GB)
somaticVep.vcf2maf_bufferSize	Int	200	The buffer size
somaticVep.vcf2maf_minHomVaf	Float	0.7	The minimum vaf for homozygous calls
somaticVep.vcf2maf_vepStats	Boolean	true	If vepStats is true, remove flag '--no_stats' from vep. If vepStats is false, running vep with flag '--no_stats'
somaticVep.vcf2maf_basename	String	basename("~{vcfFile}",".vcf.gz")	Base name
somaticVep.tumorOnlyAlign_timeout	Int	6	Hours before task timeout
somaticVep.tumorOnlyAlign_threads	Int	4	Requested CPU threads
somaticVep.tumorOnlyAlign_jobMemory	Int	32	Memory allocated for this job (GB)
somaticVep.tumorOnlyAlign_modules	String	"bcftools/1.9 tabix/0.2.6"	Required environment modules
somaticVep.tumorOnlyAlign_basename	String	basename("~{vcfFile}",".vcf.gz")	Base name
somaticVep.vep_timeout	Int	16	Hours before task timeout
somaticVep.vep_threads	Int	4	Requested CPU threads
somaticVep.vep_jobMemory	Int	32	Memory allocated for this job (GB)
somaticVep.vep_vepStats	Boolean	true	If vepStats is true, remove flag '--no_stats' from vep. If vepStats is false, running vep with flag '--no_stats'
somaticVep.vep_addParam	String?	None	Additional vep parameters
somaticVep.vep_basename	String	basename("~{vcfFile}",".vcf.gz")	Base name
somaticVep.subsetVcf_timeout	Int	6	Maximum amount of time (in hours) the task can run for.
somaticVep.subsetVcf_threads	Int	4	Requested CPU threads.
somaticVep.subsetVcf_jobMemory	Int	32	Memory allocated to job (in GB).
somaticVep.subsetVcf_modules	String	"bcftools/1.9"	Required environment modules
somaticVep.subsetVcf_basename	String	basename("~{vcfFile}",".vcf.gz")	Base name
somaticVep.chromosomeArray_timeout	Int	1	Maximum amount of time (in hours) the task can run for.
somaticVep.chromosomeArray_threads	Int	4	Requested CPU threads.
somaticVep.chromosomeArray_jobMemory	Int	1	Memory allocated to job (in GB).
somaticVep.getSampleNames_timeout	Int	1	Hours before task timeout
somaticVep.getSampleNames_threads	Int	4	Requested CPU threads
somaticVep.getSampleNames_jobMemory	Int	1	Memory allocated for this job (GB)
somaticVep.targetBedTask_timeout	Int	6	Hours before task timeout
somaticVep.targetBedTask_threads	Int	4	Requested CPU threads
somaticVep.targetBedTask_jobMemory	Int	32	Memory allocated for this job (GB)
somaticVep.targetBedTask_modules	String	"bedtools/2.27 tabix/0.2.6"	Required environment modules
somaticVep.targetBedTask_basename	String	basename("~{vcfFile}",".vcf.gz")	Base name
somaticVep.targetBed	String?	None	Target bed file
somaticFilterMaf.mafNormalFile	File?	None	input file for normal sample
somaticFilterMaf.freqList	String	"$MAF_FILTERING_ROOT/TGL.frequency.20210609.annot.txt"	frequency list used in maf annotation
somaticFilterMaf.modules	String	"python/3.9 pandas/1.4.2 maf-filtering/2024-07-10"	module for running preprocessing
somaticFilterMaf.jobMemory	Int	8	memory allocated to preprocessing, in GB
somaticFilterMaf.timeout	Int	1	timeout in hours
somaticFilterMaf.threads	Int	1	number of cpu threads to be used

Outputs

Output	Type	Description
tumorVcf	File	{'description': 'vep vcf for tumor sample', 'vidarr_label': 'tumorVcf'}
tumorVcfIndex	File	{'description': 'vep vcf index for tumor sample', 'vidarr_label': 'tumorVcfIndex'}
normalVcf	File	{'description': 'vep vcf for normal sample', 'vidarr_label': 'normalVcf'}
normalVcfIndex	File	{'description': 'vep vcf index for normal sample', 'vidarr_label': 'normalVcfIndex'}
somaticVcf	File	{'description': 'vep vcf for somatic samples', 'vidarr_label': 'somaticVcf'}
somaticVcfIndex	File	{'description': 'vep vcf index for somatic samples', 'vidarr_label': 'somaticVcfIndex'}
tumorMaf	File?	{'description': 'maf file of tumor, before filtering', 'vidarr_label': 'tumorMaf'}
normalMaf	File?	{'description': 'maf file of normal, before filtering', 'vidarr_label': 'normalMaf'}
somaticMaf	File?	{'description': 'Unfiltered maf file generated from mutect2 run in somatic mode, with matched tumor and normal', 'vidarr_label': 'somaticMaf'}
tumorFilteredMaf	File?	{'description': 'tumour Maf with normal annotation and filtering', 'vidarr_label': 'filterredMaf'}
somaticFilteredMaf	File?	{'description': 'maf file after filtering for somaticMaf', 'vidarr_label': 'somaticFilterredMaf'}

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 [email protected] .

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