BioWDL: somatic-variantcalling

A pipeline for somatic variantcalling.

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Inputs for SomaticVariantcalling

The following is an overview of all available inputs in SomaticVariantcalling.

Required inputs

SomaticVariantcalling.referenceFasta
File
The reference fasta file.
SomaticVariantcalling.referenceFastaDict
File
Sequence dictionary (.dict) file of the reference.
SomaticVariantcalling.referenceFastaFai
File
Fasta index (.fai) file of the reference.
SomaticVariantcalling.tumorBam
File
The BAM file for the tumor/case sample.
SomaticVariantcalling.tumorBamIndex
File
The index for the tumor/case sample's BAM file.
SomaticVariantcalling.tumorSample
String
The name of the tumor/case sample.

Other common inputs

SomaticVariantcalling.controlBam
File?
The BAM file for the normal/control sample.
SomaticVariantcalling.controlBamIndex
File?
The index for the normal/control sample's BAM file.
SomaticVariantcalling.controlSample
String?
The name of the normal/control sample.
SomaticVariantcalling.outputDir
String — Default: "."
The directory to which the outputs will be written.
SomaticVariantcalling.pairedSomaticSeq.exclusionRegion
File?
A bed file describing regions to exclude.
SomaticVariantcalling.pairedTraining.exclusionRegion
File?
A bed file describing regions to exclude.
SomaticVariantcalling.regions
File?
A bed file describing the regions to operate on.
SomaticVariantcalling.runManta
Boolean — Default: true
Whether or not manta should be run as part of the Strelka pipeline.
SomaticVariantcalling.runMutect2
Boolean — Default: true
Whether or not to run Mutect2.
SomaticVariantcalling.runStrelka
Boolean — Default: true
Whether or not to run Strelka.
SomaticVariantcalling.runVardict
Boolean — Default: true
Whether or not to run VarDict.
SomaticVariantcalling.singleSomaticSeq.exclusionRegion
File?
A bed file describing regions to exclude.
SomaticVariantcalling.singleTraining.exclusionRegion
File?
A bed file describing regions to exclude.
SomaticVariantcalling.strelka.exome
Boolean — Default: false
Whether or not the data is from exome sequencing.
SomaticVariantcalling.strelka.rna
Boolean — Default: false
Whether or not the data is from RNA sequencing.

Advanced inputs

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SomaticVariantcalling.combineVariants.dockerImage
String — Default: "broadinstitute/gatk3:3.8-1"
The docker image used for this task. Changing this may result in errors which the developers may choose not to address.
SomaticVariantcalling.combineVariants.filteredRecordsMergeType
String — Default: "KEEP_IF_ANY_UNFILTERED"
Equivalent to CombineVariants' `--filteredrecordsmergetype` option.
SomaticVariantcalling.combineVariants.genotypeMergeOption
String — Default: "UNIQUIFY"
Equivalent to CombineVariants' `--genotypemergeoption` option.
SomaticVariantcalling.combineVariants.javaXmx
String — Default: "12G"
The maximum memory available to the program. Should be lower than `memory` to accommodate JVM overhead.
SomaticVariantcalling.combineVariants.memory
String — Default: "13G"
The amount of memory this job will use.
SomaticVariantcalling.combineVariants.timeMinutes
Int — Default: 180
The maximum amount of time the job will run in minutes.
SomaticVariantcalling.dockerImages
Map[String,String] — Default: {"picard": "quay.io/biocontainers/picard:2.23.2--0", "gatk4": "quay.io/biocontainers/gatk4:4.1.8.0--py38h37ae868_0", "chunked-scatter": "quay.io/biocontainers/chunked-scatter:1.0.0--py_0", "tabix": "quay.io/biocontainers/tabix:0.2.6--ha92aebf_0", "manta": "quay.io/biocontainers/manta:1.4.0--py27_1", "strelka": "quay.io/biocontainers/strelka:2.9.7--0", "vardict-java": "quay.io/biocontainers/vardict-java:1.5.8--1", "somaticseq": "lethalfang/somaticseq:3.1.0", "samtools": "quay.io/biocontainers/samtools:1.10--h9402c20_2"}
The docker images used. Changing this may result in errors which the developers may choose not to address.
SomaticVariantcalling.indelIndex.memory
String — Default: "2G"
The amount of memory this job will use.
SomaticVariantcalling.indelIndex.timeMinutes
Int — Default: 1 + ceil(size(inputFile,"G"))
The maximum amount of time the job will run in minutes.
SomaticVariantcalling.mutect2.calculateContamination.javaXmx
String — Default: "12G"
The maximum memory available to the program. Should be lower than `memory` to accommodate JVM overhead.
SomaticVariantcalling.mutect2.calculateContamination.memory
String — Default: "13G"
The amount of memory this job will use.
SomaticVariantcalling.mutect2.calculateContamination.timeMinutes
Int — Default: 180
The maximum amount of time the job will run in minutes.
SomaticVariantcalling.mutect2.filterMutectCalls.javaXmx
String — Default: "12G"
The maximum memory available to the program. Should be lower than `memory` to accommodate JVM overhead.
SomaticVariantcalling.mutect2.filterMutectCalls.memory
String — Default: "13G"
The amount of memory this job will use.
SomaticVariantcalling.mutect2.filterMutectCalls.timeMinutes
Int — Default: 60
The maximum amount of time the job will run in minutes.
SomaticVariantcalling.mutect2.filterMutectCalls.uniqueAltReadCount
Int — Default: 4
Equivalent to FilterMutectCalls' `--unique-alt-read-count` option.
SomaticVariantcalling.mutect2.gatherVcfs.compressionLevel
Int — Default: 1
The compression level at which the BAM files are written.
SomaticVariantcalling.mutect2.gatherVcfs.javaXmx
String — Default: "4G"
The maximum memory available to the program. Should be lower than `memory` to accommodate JVM overhead.
SomaticVariantcalling.mutect2.gatherVcfs.memory
String — Default: "5G"
The amount of memory this job will use.
SomaticVariantcalling.mutect2.gatherVcfs.timeMinutes
Int — Default: 1 + ceil(size(inputVCFs,"G")) * 2
The maximum amount of time the job will run in minutes.
SomaticVariantcalling.mutect2.gatherVcfs.useJdkDeflater
Boolean — Default: true
True, uses the java deflator to compress the BAM files. False uses the optimized intel deflater.
SomaticVariantcalling.mutect2.gatherVcfs.useJdkInflater
Boolean — Default: true
True, uses the java inflater. False, uses the optimized intel inflater.
SomaticVariantcalling.mutect2.getPileupSummariesNormal.javaXmx
String — Default: "12G"
The maximum memory available to the program. Should be lower than `memory` to accommodate JVM overhead.
SomaticVariantcalling.mutect2.getPileupSummariesNormal.memory
String — Default: "13G"
The amount of memory this job will use.
SomaticVariantcalling.mutect2.getPileupSummariesNormal.timeMinutes
Int — Default: 120
The maximum amount of time the job will run in minutes.
SomaticVariantcalling.mutect2.getPileupSummariesTumor.javaXmx
String — Default: "12G"
The maximum memory available to the program. Should be lower than `memory` to accommodate JVM overhead.
SomaticVariantcalling.mutect2.getPileupSummariesTumor.memory
String — Default: "13G"
The amount of memory this job will use.
SomaticVariantcalling.mutect2.getPileupSummariesTumor.timeMinutes
Int — Default: 120
The maximum amount of time the job will run in minutes.
SomaticVariantcalling.mutect2.learnReadOrientationModel.javaXmx
String — Default: "12G"
The maximum memory available to the program. Should be lower than `memory` to accommodate JVM overhead.
SomaticVariantcalling.mutect2.learnReadOrientationModel.memory
String — Default: "13G"
The amount of memory this job will use.
SomaticVariantcalling.mutect2.learnReadOrientationModel.timeMinutes
Int — Default: 120
The maximum amount of time the job will run in minutes.
SomaticVariantcalling.mutect2.mergeStats.javaXmx
String — Default: "14G"
The maximum memory available to the program. Should be lower than `memory` to accommodate JVM overhead.
SomaticVariantcalling.mutect2.mergeStats.memory
String — Default: "15G"
The amount of memory this job will use.
SomaticVariantcalling.mutect2.mergeStats.timeMinutes
Int — Default: 30
The maximum amount of time the job will run in minutes.
SomaticVariantcalling.mutect2.mutect2.f1r2TarGz
String — Default: "f1r2.tar.gz"
Equivalent to Mutect2's `--f1r2-tar-gz` option.
SomaticVariantcalling.mutect2.mutect2.germlineResource
File?
Equivalent to Mutect2's `--germline-resource` option.
SomaticVariantcalling.mutect2.mutect2.germlineResourceIndex
File?
The index for the germline resource.
SomaticVariantcalling.mutect2.mutect2.javaXmx
String — Default: "4G"
The maximum memory available to the program. Should be lower than `memory` to accommodate JVM overhead.
SomaticVariantcalling.mutect2.mutect2.memory
String — Default: "5G"
The amount of memory this job will use.
SomaticVariantcalling.mutect2.mutect2.outputStats
String — Default: outputVcf + ".stats"
The location the output statistics should be written to.
SomaticVariantcalling.mutect2.mutect2.panelOfNormals
File?
Equivalent to Mutect2's `--panel-of-normals` option.
SomaticVariantcalling.mutect2.mutect2.panelOfNormalsIndex
File?
The index for the panel of normals.
SomaticVariantcalling.mutect2.mutect2.timeMinutes
Int — Default: 240
The maximum amount of time the job will run in minutes.
SomaticVariantcalling.mutect2.scatterList.memory
String — Default: "256M"
The amount of memory this job will use.
SomaticVariantcalling.mutect2.scatterList.prefix
String — Default: "scatters/scatter-"
The prefix of the ouput files. Output will be named like: .bed, in which N is an incrementing number. Default 'scatter-'. </dd>
SomaticVariantcalling.mutect2.scatterList.timeMinutes
Int — Default: 2
The maximum amount of time the job will run in minutes.
SomaticVariantcalling.mutect2.scatterSize
Int?
The size of the scattered regions in bases. Scattering is used to speed up certain processes. The genome will be seperated into multiple chunks (scatters) which will be processed in their own job, allowing for parallel processing. Higher values will result in a lower number of jobs. The optimal value here will depend on the available resources.
SomaticVariantcalling.mutect2.scatterSizeMillions
Int — Default: 1000
Same as scatterSize, but is multiplied by 1000000 to get scatterSize. This allows for setting larger values more easily
SomaticVariantcalling.pairedSomaticSeq.jsmVCF
File?
A VCF as produced by jsm.
SomaticVariantcalling.pairedSomaticSeq.lofreqIndel
File?
An indel VCF as produced by lofreq.
SomaticVariantcalling.pairedSomaticSeq.lofreqSNV
File?
An SNV VCF as produced by lofreq.
SomaticVariantcalling.pairedSomaticSeq.memory
String — Default: "2G"
The amount of memory this job will use.
SomaticVariantcalling.pairedSomaticSeq.museVCF
File?
A VCF as produced by muse.
SomaticVariantcalling.pairedSomaticSeq.scalpelVCF
File?
A VCF as produced by scalpel.
SomaticVariantcalling.pairedSomaticSeq.somaticsniperVCF
File?
A VCF as produced by somaticsniper.
SomaticVariantcalling.pairedSomaticSeq.threads
Int — Default: 1
The number of threads to use.
SomaticVariantcalling.pairedSomaticSeq.timeMinutes
Int — Default: 60
The maximum amount of time the job will run in minutes.
SomaticVariantcalling.pairedSomaticSeq.varscanIndel
File?
An indel VCF as produced by varscan.
SomaticVariantcalling.pairedSomaticSeq.varscanSNV
File?
An SNV VCF as produced by varscan.
SomaticVariantcalling.pairedTraining.memory
String — Default: "2G"
The amount of memory this job will use.
SomaticVariantcalling.pairedTraining.threads
Int — Default: 1
The number of threads to use.
SomaticVariantcalling.pairedTraining.timeMinutes
Int — Default: 240
The maximum amount of time the job will run in minutes.
SomaticVariantcalling.runCombineVariants
Boolean — Default: false
Whether or not to combine the variant calling results into one VCF file.
SomaticVariantcalling.singleSomaticSeq.lofreqVCF
File?
A VCF as produced by lofreq.
SomaticVariantcalling.singleSomaticSeq.memory
String — Default: "2G"
The amount of memory this job will use.
SomaticVariantcalling.singleSomaticSeq.scalpelVCF
File?
A VCF as produced by scalpel.
SomaticVariantcalling.singleSomaticSeq.threads
Int — Default: 1
The number of threads to use.
SomaticVariantcalling.singleSomaticSeq.timeMinutes
Int — Default: 60
The maximum amount of time the job will run in minutes.
SomaticVariantcalling.singleSomaticSeq.varscanVCF
File?
A VCF as produced by varscan.
SomaticVariantcalling.singleTraining.memory
String — Default: "2G"
The amount of memory this job will use.
SomaticVariantcalling.singleTraining.threads
Int — Default: 1
The number of threads to use.
SomaticVariantcalling.singleTraining.timeMinutes
Int — Default: 240
The maximum amount of time the job will run in minutes.
SomaticVariantcalling.sitesForContamination
File?
A bed file, vcf file or interval list with regions for GetPileupSummaries to operate on.
SomaticVariantcalling.sitesForContaminationIndex
File?
The index for the vcf file provided to sitesForContamination.
SomaticVariantcalling.snvIndex.memory
String — Default: "2G"
The amount of memory this job will use.
SomaticVariantcalling.snvIndex.timeMinutes
Int — Default: 1 + ceil(size(inputFile,"G"))
The maximum amount of time the job will run in minutes.
SomaticVariantcalling.strelka.addGTFieldIndels.memory
String — Default: "2G"
The amount of memory this job will use.
SomaticVariantcalling.strelka.addGTFieldIndels.outputVCFName
String — Default: basename(strelkaVCF,".gz")
The location the output VCF file should be written to.
SomaticVariantcalling.strelka.addGTFieldIndels.timeMinutes
Int — Default: 20
The maximum amount of time the job will run in minutes.
SomaticVariantcalling.strelka.addGTFieldSVs.memory
String — Default: "2G"
The amount of memory this job will use.
SomaticVariantcalling.strelka.addGTFieldSVs.outputVCFName
String — Default: basename(strelkaVCF,".gz")
The location the output VCF file should be written to.
SomaticVariantcalling.strelka.addGTFieldSVs.timeMinutes
Int — Default: 20
The maximum amount of time the job will run in minutes.
SomaticVariantcalling.strelka.addGTFieldVariants.memory
String — Default: "2G"
The amount of memory this job will use.
SomaticVariantcalling.strelka.addGTFieldVariants.outputVCFName
String — Default: basename(strelkaVCF,".gz")
The location the output VCF file should be written to.
SomaticVariantcalling.strelka.addGTFieldVariants.timeMinutes
Int — Default: 20
The maximum amount of time the job will run in minutes.
SomaticVariantcalling.strelka.bedPrepare.memory
String — Default: "2G"
The amount of memory this job will use.
SomaticVariantcalling.strelka.bedPrepare.timeMinutes
Int — Default: 1 + ceil(size(inputFile,"G"))
The maximum amount of time the job will run in minutes.
SomaticVariantcalling.strelka.combineVariants.dockerImage
String — Default: "broadinstitute/gatk3:3.8-1"
The docker image used for this task. Changing this may result in errors which the developers may choose not to address.
SomaticVariantcalling.strelka.combineVariants.filteredRecordsMergeType
String — Default: "KEEP_IF_ANY_UNFILTERED"
Equivalent to CombineVariants' `--filteredrecordsmergetype` option.
SomaticVariantcalling.strelka.combineVariants.genotypeMergeOption
String — Default: "UNIQUIFY"
Equivalent to CombineVariants' `--genotypemergeoption` option.
SomaticVariantcalling.strelka.combineVariants.javaXmx
String — Default: "12G"
The maximum memory available to the program. Should be lower than `memory` to accommodate JVM overhead.
SomaticVariantcalling.strelka.combineVariants.memory
String — Default: "13G"
The amount of memory this job will use.
SomaticVariantcalling.strelka.combineVariants.timeMinutes
Int — Default: 180
The maximum amount of time the job will run in minutes.
SomaticVariantcalling.strelka.gatherIndels.compressionLevel
Int — Default: 1
The compression level at which the BAM files are written.
SomaticVariantcalling.strelka.gatherIndels.javaXmx
String — Default: "4G"
The maximum memory available to the program. Should be lower than `memory` to accommodate JVM overhead.
SomaticVariantcalling.strelka.gatherIndels.memory
String — Default: "5G"
The amount of memory this job will use.
SomaticVariantcalling.strelka.gatherIndels.timeMinutes
Int — Default: 1 + ceil(size(inputVCFs,"G")) * 2
The maximum amount of time the job will run in minutes.
SomaticVariantcalling.strelka.gatherIndels.useJdkDeflater
Boolean — Default: true
True, uses the java deflator to compress the BAM files. False uses the optimized intel deflater.
SomaticVariantcalling.strelka.gatherIndels.useJdkInflater
Boolean — Default: true
True, uses the java inflater. False, uses the optimized intel inflater.
SomaticVariantcalling.strelka.gatherSVs.compressionLevel
Int — Default: 1
The compression level at which the BAM files are written.
SomaticVariantcalling.strelka.gatherSVs.javaXmx
String — Default: "4G"
The maximum memory available to the program. Should be lower than `memory` to accommodate JVM overhead.
SomaticVariantcalling.strelka.gatherSVs.memory
String — Default: "5G"
The amount of memory this job will use.
SomaticVariantcalling.strelka.gatherSVs.timeMinutes
Int — Default: 1 + ceil(size(inputVCFs,"G")) * 2
The maximum amount of time the job will run in minutes.
SomaticVariantcalling.strelka.gatherSVs.useJdkDeflater
Boolean — Default: true
True, uses the java deflator to compress the BAM files. False uses the optimized intel deflater.
SomaticVariantcalling.strelka.gatherSVs.useJdkInflater
Boolean — Default: true
True, uses the java inflater. False, uses the optimized intel inflater.
SomaticVariantcalling.strelka.gatherVariants.compressionLevel
Int — Default: 1
The compression level at which the BAM files are written.
SomaticVariantcalling.strelka.gatherVariants.javaXmx
String — Default: "4G"
The maximum memory available to the program. Should be lower than `memory` to accommodate JVM overhead.
SomaticVariantcalling.strelka.gatherVariants.memory
String — Default: "5G"
The amount of memory this job will use.
SomaticVariantcalling.strelka.gatherVariants.timeMinutes
Int — Default: 1 + ceil(size(inputVCFs,"G")) * 2
The maximum amount of time the job will run in minutes.
SomaticVariantcalling.strelka.gatherVariants.useJdkDeflater
Boolean — Default: true
True, uses the java deflator to compress the BAM files. False uses the optimized intel deflater.
SomaticVariantcalling.strelka.gatherVariants.useJdkInflater
Boolean — Default: true
True, uses the java inflater. False, uses the optimized intel inflater.
SomaticVariantcalling.strelka.indelsIndex.memory
String — Default: "2G"
The amount of memory this job will use.
SomaticVariantcalling.strelka.indelsIndex.timeMinutes
Int — Default: 1 + ceil(size(inputFile,"G"))
The maximum amount of time the job will run in minutes.
SomaticVariantcalling.strelka.mantaSomatic.cores
Int — Default: 1
The number of cores to use.
SomaticVariantcalling.strelka.mantaSomatic.memoryGb
Int — Default: 4
The amount of memory this job will use in Gigabytes.
SomaticVariantcalling.strelka.mantaSomatic.timeMinutes
Int — Default: 60
The maximum amount of time the job will run in minutes.
SomaticVariantcalling.strelka.scatterList.memory
String — Default: "256M"
The amount of memory this job will use.
SomaticVariantcalling.strelka.scatterList.prefix
String — Default: "scatters/scatter-"
The prefix of the ouput files. Output will be named like: .bed, in which N is an incrementing number. Default 'scatter-'. </dd>
SomaticVariantcalling.strelka.scatterList.timeMinutes
Int — Default: 2
The maximum amount of time the job will run in minutes.
SomaticVariantcalling.strelka.scatterSize
Int?
The size of the scattered regions in bases. Scattering is used to speed up certain processes. The genome will be seperated into multiple chunks (scatters) which will be processed in their own job, allowing for parallel processing. Higher values will result in a lower number of jobs. The optimal value here will depend on the available resources.
SomaticVariantcalling.strelka.scatterSizeMillions
Int — Default: 1000
Same as scatterSize, but is multiplied by 1000000 to get scatterSize. This allows for setting larger values more easily
SomaticVariantcalling.strelka.strelkaGermline.cores
Int — Default: 1
The number of cores to use.
SomaticVariantcalling.strelka.strelkaGermline.memoryGb
Int — Default: 4
The amount of memory this job will use in Gigabytes.
SomaticVariantcalling.strelka.strelkaGermline.timeMinutes
Int — Default: 90
The maximum amount of time the job will run in minutes.
SomaticVariantcalling.strelka.strelkaSomatic.cores
Int — Default: 1
The number of cores to use.
SomaticVariantcalling.strelka.strelkaSomatic.memoryGb
Int — Default: 4
The amount of memory this job will use in Gigabytes.
SomaticVariantcalling.strelka.strelkaSomatic.timeMinutes
Int — Default: 90
The maximum amount of time the job will run in minutes.
SomaticVariantcalling.strelka.svsIndex.memory
String — Default: "2G"
The amount of memory this job will use.
SomaticVariantcalling.strelka.svsIndex.timeMinutes
Int — Default: 1 + ceil(size(inputFile,"G"))
The maximum amount of time the job will run in minutes.
SomaticVariantcalling.strelka.variantsIndex.memory
String — Default: "2G"
The amount of memory this job will use.
SomaticVariantcalling.strelka.variantsIndex.timeMinutes
Int — Default: 1 + ceil(size(inputFile,"G"))
The maximum amount of time the job will run in minutes.
SomaticVariantcalling.trainingSet
struct(jsmVCF : File?, lofreqIndel : File?, lofreqSNV : File?, museVCF : File?, mutect2VCF : File?, normalBam : File?, normalBamIndex : File?, scalpelVCF : File?, somaticsniperVCF : File?, strelkaIndel : File?, strelkaSNV : File?, truthIndel : File, truthSNV : File, tumorBam : File, tumorBamIndex : File, vardictVCF : File?, varscanIndel : File?, varscanSNV : File?)?
VCF files used to train somaticseq.
SomaticVariantcalling.vardict.filterSupplementaryAlignments
Boolean — Default: false
Whether or not supplementary reads should be filtered before vardict is run.
SomaticVariantcalling.vardict.filterSupplementaryControl.excludeSpecificFilter
Int?
Equivalent to samtools view's `-G` option.
SomaticVariantcalling.vardict.filterSupplementaryControl.includeFilter
Int?
Equivalent to samtools view's `-f` option.
SomaticVariantcalling.vardict.filterSupplementaryControl.MAPQthreshold
Int?
Equivalent to samtools view's `-q` option.
SomaticVariantcalling.vardict.filterSupplementaryControl.memory
String — Default: "1G"
The amount of memory this job will use.
SomaticVariantcalling.vardict.filterSupplementaryControl.referenceFasta
File?
The reference fasta file also used for mapping.
SomaticVariantcalling.vardict.filterSupplementaryControl.threads
Int — Default: 1
The number of threads to use.
SomaticVariantcalling.vardict.filterSupplementaryControl.timeMinutes
Int — Default: 1 + ceil((size(inFile,"G") * 5))
The maximum amount of time the job will run in minutes.
SomaticVariantcalling.vardict.filterSupplementaryControl.uncompressedBamOutput
Boolean — Default: false
Equivalent to samtools view's `-u` flag.
SomaticVariantcalling.vardict.filterSupplementaryTumor.excludeSpecificFilter
Int?
Equivalent to samtools view's `-G` option.
SomaticVariantcalling.vardict.filterSupplementaryTumor.includeFilter
Int?
Equivalent to samtools view's `-f` option.
SomaticVariantcalling.vardict.filterSupplementaryTumor.MAPQthreshold
Int?
Equivalent to samtools view's `-q` option.
SomaticVariantcalling.vardict.filterSupplementaryTumor.memory
String — Default: "1G"
The amount of memory this job will use.
SomaticVariantcalling.vardict.filterSupplementaryTumor.referenceFasta
File?
The reference fasta file also used for mapping.
SomaticVariantcalling.vardict.filterSupplementaryTumor.threads
Int — Default: 1
The number of threads to use.
SomaticVariantcalling.vardict.filterSupplementaryTumor.timeMinutes
Int — Default: 1 + ceil((size(inFile,"G") * 5))
The maximum amount of time the job will run in minutes.
SomaticVariantcalling.vardict.filterSupplementaryTumor.uncompressedBamOutput
Boolean — Default: false
Equivalent to samtools view's `-u` flag.
SomaticVariantcalling.vardict.gatherVcfs.javaXmx
String — Default: "8G"
The maximum memory available to the program. Should be lower than `memory` to accommodate JVM overhead.
SomaticVariantcalling.vardict.gatherVcfs.memory
String — Default: "9G"
The amount of memory this job will use.
SomaticVariantcalling.vardict.gatherVcfs.timeMinutes
Int — Default: 1 + ceil((size(vcfFiles,"G") * 5))
The maximum amount of time the job will run in minutes.
SomaticVariantcalling.vardict.scatterList.chunkSize
Int?
Equivalent to chunked-scatter's `-c` option.
SomaticVariantcalling.vardict.scatterList.memory
String — Default: "256M"
The amount of memory this job will use.
SomaticVariantcalling.vardict.scatterList.minimumBasesPerFile
Int?
Equivalent to chunked-scatter's `-m` option.
SomaticVariantcalling.vardict.scatterList.overlap
Int?
Equivalent to chunked-scatter's `-o` option.
SomaticVariantcalling.vardict.scatterList.prefix
String — Default: "./scatter"
The prefix for the output files.
SomaticVariantcalling.vardict.scatterList.splitContigs
Boolean — Default: false
If set, contigs are allowed to be split up over multiple files.
SomaticVariantcalling.vardict.scatterList.timeMinutes
Int — Default: 2
The maximum amount of time the job will run in minutes.
SomaticVariantcalling.vardict.varDict.chromosomeColumn
Int — Default: 1
Equivalent to vardict-java's `-c` option.
SomaticVariantcalling.vardict.varDict.endColumn
Int — Default: 3
Equivalent to vardict-java's `-E` option.
SomaticVariantcalling.vardict.varDict.geneColumn
Int — Default: 4
Equivalent to vardict-java's `-g` option.
SomaticVariantcalling.vardict.varDict.javaXmx
String — Default: "16G"
The maximum memory available to the program. Should be lower than `memory` to accommodate JVM overhead.
SomaticVariantcalling.vardict.varDict.mappingQuality
Float — Default: 20
Equivalent to var2vcf_paired.pl or var2vcf_valid.pl's `-Q` option.
SomaticVariantcalling.vardict.varDict.memory
String — Default: "18G"
The amount of memory this job will use.
SomaticVariantcalling.vardict.varDict.minimumAlleleFrequency
Float — Default: 0.02
Equivalent to var2vcf_paired.pl or var2vcf_valid.pl's `-f` option.
SomaticVariantcalling.vardict.varDict.minimumTotalDepth
Int — Default: 8
Equivalent to var2vcf_paired.pl or var2vcf_valid.pl's `-d` option.
SomaticVariantcalling.vardict.varDict.minimumVariantDepth
Int — Default: 4
Equivalent to var2vcf_paired.pl or var2vcf_valid.pl's `-v` option.
SomaticVariantcalling.vardict.varDict.outputAllVariantsAtSamePosition
Boolean — Default: true
Equivalent to var2vcf_paired.pl or var2vcf_valid.pl's `-A` flag.
SomaticVariantcalling.vardict.varDict.outputCandidateSomaticOnly
Boolean — Default: true
Equivalent to var2vcf_paired.pl or var2vcf_valid.pl's `-M` flag.
SomaticVariantcalling.vardict.varDict.startColumn
Int — Default: 2
Equivalent to vardict-java's `-S` option.
SomaticVariantcalling.vardict.varDict.threads
Int — Default: 1
The number of threads to use.
SomaticVariantcalling.vardict.varDict.timeMinutes
Int — Default: 300
The maximum amount of time the job will run in minutes.
SomaticVariantcalling.variantsForContamination
File?
A VCF file with common variants.
SomaticVariantcalling.variantsForContaminationIndex
File?
The index of the common variants VCF file.
</dl> </details> ## Do not set these inputs! The following inputs should ***not*** be set, even though womtool may show them as being available inputs. * SomaticVariantcalling.DONOTDEFINETHIS * SomaticVariantcalling.indelIndex.type * SomaticVariantcalling.snvIndex.type * SomaticVariantcalling.strelka.indelsIndex.type * SomaticVariantcalling.strelka.svsIndex.type * SomaticVariantcalling.strelka.variantsIndex.type * SomaticVariantcalling.strelka.strelkaSomatic.doNotDefineThis