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
`outputFileNamePrefix`	String	Prefix to use for output file
`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
`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	Extra arguments
`mutect2.mergeStats_timeout`	Int	5	Hours before task timeout
`mutect2.mergeStats_memory`	Int	4	Memory allocated for job
`mutect2.mergeStats_modules`	String	"gatk/4.1.6.0"	Names and versions of modules to load
`mutect2.mergeVCFs_timeout`	Int	12	Hours before task timeout
`mutect2.mergeVCFs_memory`	Int	4	Memory allocated for job
`mutect2.runMutect2_timeout`	Int	24	Hours before task timeout
`mutect2.runMutect2_memory`	Int	32	Memory allocated for job
`mutect2.runMutect2_threads`	Int	4	Number of threads to request
`mutect2.runMutect2_mutect2ExtraArgs`	String?	None	Extra arguments
`mutect2.runMutect2_mutectTag`	String	"mutect2"	Tag
`mutect2.splitStringToArray_modules`	String	""	Names and versions of modules to load
`mutect2.splitStringToArray_timeout`	Int	1	Hours before task timeout
`mutect2.splitStringToArray_memory`	Int	1	Memory allocated for job
`mutect2.splitStringToArray_lineSeparator`	String	","	line separator
`mutect2.normalBam`	File?	None	Input normal file (bam or sam)
`mutect2.normalBai`	File?	None	Index file for normal bam
`mutect2.pon`	File?	None	pon
`mutect2.ponIdx`	File?	None	pon ID
`mutect2.gnomad`	File?	None	gnomad
`mutect2.gnomadIdx`	File?	None	gnomad ID
`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_species`	String	"homo_sapiens"	Species name
`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_species`	String	"homo_sapiens"	Species name
`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	Extra arguments
`matchedMutect2.mergeStats_timeout`	Int	5	Hours before task timeout
`matchedMutect2.mergeStats_memory`	Int	4	Memory allocated for job
`matchedMutect2.mergeStats_modules`	String	"gatk/4.1.6.0"	Names and versions of modules to load
`matchedMutect2.mergeVCFs_timeout`	Int	12	Hours before task timeout
`matchedMutect2.mergeVCFs_memory`	Int	4	Memory allocated for job
`matchedMutect2.runMutect2_timeout`	Int	24	Hours before task timeout
`matchedMutect2.runMutect2_memory`	Int	32	Memory allocated for job
`matchedMutect2.runMutect2_threads`	Int	4	Number of threads to request
`matchedMutect2.runMutect2_mutect2ExtraArgs`	String?	None	Extra arguments
`matchedMutect2.runMutect2_mutectTag`	String	"mutect2"	Tag
`matchedMutect2.splitStringToArray_modules`	String	""	Names and versions of modules to load
`matchedMutect2.splitStringToArray_timeout`	Int	1	Hours before task timeout
`matchedMutect2.splitStringToArray_memory`	Int	1	Memory allocated for job
`matchedMutect2.splitStringToArray_lineSeparator`	String	","	line separator
`matchedMutect2.pon`	File?	None	pon
`matchedMutect2.ponIdx`	File?	None	pon ID
`matchedMutect2.gnomad`	File?	None	gnomad
`matchedMutect2.gnomadIdx`	File?	None	gnomad ID
`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_species`	String	"homo_sapiens"	Species name
`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_species`	String	"homo_sapiens"	Species name
`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.normalName`	String?	None	Name of the normal sample
`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
`tumorDcsScVcf`	File	DCS vcf for tumor sample
`tumorDcsScVcfIndex`	File	DCS vcf index for tumor sample
`tumorSscsScVcf`	File	SSCS vcf for tumor sample
`tumorSscsScVcfIndex`	File	SSCS vcf index for tumor sample
`tumorAllUniqueVcf`	File	vcf of DCS + singletons for tumor sample
`tumorAllUniqueVcfIndex`	File	vcf index for DCS + singletons for tumor sample
`tumorVepVcf`	File	vep vcf for tumor sample
`tumorVepVcfIndex`	File	vep vcf index for tumor sample
`tumorMafOutput`	File?	maf output for tumor sample
`normalDcsScVcf`	File	DCS vcf for normal sample
`normalDcsScVcfIndex`	File	DCS vcf index for normal sample
`normalSscsScVcf`	File	SSCS vcf for normal sample
`normalSscsScVcfIndex`	File	SSCS vcf index for normal sample
`normalAllUniqueVcf`	File	vcf of DCS + singletons for tumor sample
`normalAllUniqueVcfIndex`	File	vcf index for DCS + singletons for tumor sample
`normalVepVcf`	File	vep vcf for normal sample
`normalVepVcfIndex`	File	vep vcf index for normal sample
`normalMafOutput`	File?	maf output for normal sample
`matchedDcsScVcf`	File	DCS vcf for matched samples
`matchedDcsScVcfIndex`	File	DCS vcf index for matched samples
`matchedSscsScVcf`	File	SSCS vcf for matched samples
`matchedSscsScVcfIndex`	File	SSCS vcf index for matched samples
`matchedAllUniqueVcf`	File	vcf of DCS + singletons for matched samples
`matchedAllUniqueVcfIndex`	File	vcf index for DCS + singletons for matched samples
`matchedVepVcf`	File	vep vcf for matched samples
`matchedVepVcfIndex`	File	vep vcf index for matched samples
`matchedMafOutput`	File?	maf output for matched samples
`filterredMaf`	File?	maf file after filtering
`matchedFilterredMaf`	File?	maf file after filtering for matched maf(maf file of matched tumor/normal version)

Commands

This section lists command(s) run by WORKFLOW workflow

Running WORKFLOW

 
 <<<
   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] .

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

Name		Name	Last commit message	Last commit date
Latest commit History 20 Commits
imports		imports
subworkflows		subworkflows
tests		tests
.gitmodules		.gitmodules
CHANGELOG.md		CHANGELOG.md
Jenkinsfile		Jenkinsfile
README.md		README.md
commands.txt		commands.txt
imports.zip		imports.zip
mutect2Consensus.wdl		mutect2Consensus.wdl
vidarrbuild.json		vidarrbuild.json
vidarrtest-regression.json.in		vidarrtest-regression.json.in

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mutect2Consensus

Overview

Dependencies

Usage

Cromwell

Inputs

Required workflow parameters:

Optional workflow parameters:

Optional task parameters:

Outputs

Commands

Support

About

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Contributors 2

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oicr-gsi/mutect2Consensus

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mutect2Consensus

Overview

Dependencies

Usage

Cromwell

Inputs

Required workflow parameters:

Optional workflow parameters:

Optional task parameters:

Outputs

Commands

Support

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