strelkaSomatic

Strelka variant caller in somatic mode

Overview

Dependencies

Usage

Cromwell

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

Inputs

Required workflow parameters:

Parameter	Value	Description
`tumorBam`	File	Input BAM file with tumor data
`tumorBai`	File	BAM index file for tumor data
`normalBam`	File	Input BAM file with normal data
`normalBai`	File	BAM index file for normal data
`reference`	String	Reference assembly id

Optional workflow parameters:

Parameter	Value	Default	Description
`bedFile`	String?	None	BED file designating regions to process
`numChunk`	Int?	None	If BED file given, number of chunks in which to split each chromosome
`outputFileNamePrefix`	String	"strelkaSomatic"	Prefix for output files

Optional task parameters:

Parameter	Value	Default	Description
`splitIntervals.gatk`	String	"$GATK_ROOT/bin/gatk"	GATK executable path
`splitIntervals.splitIntervalsExtraArgs`	String?	None	Additional arguments for the 'gatk SplitIntervals' command
`splitIntervals.nonRefModules`	String	"gatk/4.1.2.0"	Environment modules other than the genome refence
`splitIntervals.memory`	Int	32	Memory allocated for job
`splitIntervals.overhead`	Int	8	Memory overhead for running on a node
`splitIntervals.timeout`	Int	72	Hours before task timeout
`convertIntervalsToBed.modules`	String	"python/3.7"	Environment modules
`convertIntervalsToBed.memory`	Int	16	Memory allocated for job
`convertIntervalsToBed.timeout`	Int	4	Hours before task timeout
`configureAndRunParallel.nonRefModules`	String	"python/2.7 samtools/1.9 strelka/2.9.10"	Environment module names other than genome reference
`configureAndRunParallel.jobMemory`	Int	16	Memory allocated for job
`configureAndRunParallel.threads`	Int	4	Number of threads for processing
`configureAndRunParallel.timeout`	Int	4	Hours before task timeout
`snvsVcfGather.modules`	String	"gatk/4.1.2.0"	Environment module names and version to load (space separated) before command execution
`snvsVcfGather.gatk`	String	"$GATK_ROOT/bin/gatk"	GATK to use
`snvsVcfGather.memory`	Int	16	Memory allocated for job
`snvsVcfGather.timeout`	Int	12	Hours before task timeout
`indelsVcfGather.modules`	String	"gatk/4.1.2.0"	Environment module names and version to load (space separated) before command execution
`indelsVcfGather.gatk`	String	"$GATK_ROOT/bin/gatk"	GATK to use
`indelsVcfGather.memory`	Int	16	Memory allocated for job
`indelsVcfGather.timeout`	Int	12	Hours before task timeout

Outputs

Output	Type	Description	Labels
`snvsVcf`	File	VCF file with SNVs, .gz compressed	vidarr_label: snvsVcf
`indelsVcf`	File	VCF file with indels, .gz compressed	vidarr_label: indelsVcf

Commands

This section lists command(s) run by strelkaSomatic workflow

Running strelkaSomatic

Main task, configuring and running Strelka2

 	set -eo pipefail
 
 	~{writeBed}
 	~{indexFeatureFile}
 
 	configureStrelkaSomaticWorkflow.py \
 	--normalBam ~{normalBam} \
 	--tumorBam ~{tumorBam} \
 	--referenceFasta ~{refFasta} \
 	~{regionsBedArg} \
 	--runDir .
 
 	./runWorkflow.py -m local -j ~{threads}

Converting interval files to .bed

.bed files use 0-based index, we need to do a proper conversion of interval files

         python3 <<CODE
         import os, re
         intervalFiles = re.split(",", "~{sep=',' intervalFiles}")
         for intervalFile in intervalFiles:
             items = re.split("\.", os.path.basename(intervalFile))
             items.pop() # remove .interval_list suffix
             bedName = ".".join(items)+".bed"
             with open(intervalFile, 'r') as inFile, open(bedName, 'w') as outFile:
                 for line in inFile:
                     if not re.match("@", line): # omit the GATK header
                         fields = re.split("\t", line.strip())
                         fields[1] = str(int(fields[1]) - 1)
                         outFile.write("\t".join(fields)+"\n")
         CODE

Splitting intervals

SplitIntervals is used to produce a requested number of files to make the analysis parallel, decreasing demand for resources per chunk and improving speed

 	set -eo pipefail
 
 	mkdir interval-files
 	ln -s ~{refFai}
 	ln -s ~{refDict}
 	~{gatk} --java-options "-Xmx~{memory-8}g" SplitIntervals \
 	-R ~{refFasta} \
 	~{intervalsArg} \
 	~{scatterArg} \
 	--subdivision-mode BALANCING_WITHOUT_INTERVAL_SUBDIVISION \
 	-O interval-files \
 	~{splitIntervalsExtraArgs}
 
 	cp interval-files/*.interval_list .

Combining vcf files after scatter

This task uses GatherVcfs tools from GATK suite which needs the files to be ordered. No overlap between covered features allowed.

    set -eo pipefail
 
    ~{gatk} GatherVcfs \
    -I ~{sep=" -I " vcfs} \
    -R ~{refFasta}
    -O ~{outputName}
 
    gzip ~{outputName}

Support

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

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oicr-gsi/strelkaSomatic