BioWDL: somatic-variantcalling

A pipeline for somatic variantcalling.

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Inputs for Mutect2

The following is an overview of all available inputs in Mutect2.

Required inputs

Mutect2.referenceFasta
File
The reference fasta file.
Mutect2.referenceFastaDict
File
Sequence dictionary (.dict) file of the reference.
Mutect2.referenceFastaFai
File
Fasta index (.fai) file of the reference.
Mutect2.tumorBam
File
The BAM file for the tumor/case sample.
Mutect2.tumorBamIndex
File
The index for the tumor/case sample's BAM file.
Mutect2.tumorSample
String
The name of the tumor/case sample.

Other common inputs

Mutect2.controlBam
File?
The BAM file for the normal/control sample.
Mutect2.controlBamIndex
File?
The index for the normal/control sample's BAM file.
Mutect2.controlSample
String?
The name of the normal/control sample.
Mutect2.outputDir
String — Default: "."
The directory to which the outputs will be written.
Mutect2.regions
File?
A bed file describing the regions to operate on.

Advanced inputs

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Mutect2.calculateContamination.javaXmx
String — Default: "12G"
The maximum memory available to the program. Should be lower than `memory` to accommodate JVM overhead.
Mutect2.calculateContamination.memory
String — Default: "13G"
The amount of memory this job will use.
Mutect2.calculateContamination.timeMinutes
Int — Default: 180
The maximum amount of time the job will run in minutes.
Mutect2.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"}
The docker images used. Changing this may result in errors which the developers may choose not to address.
Mutect2.filterMutectCalls.javaXmx
String — Default: "12G"
The maximum memory available to the program. Should be lower than `memory` to accommodate JVM overhead.
Mutect2.filterMutectCalls.memory
String — Default: "13G"
The amount of memory this job will use.
Mutect2.filterMutectCalls.timeMinutes
Int — Default: 60
The maximum amount of time the job will run in minutes.
Mutect2.filterMutectCalls.uniqueAltReadCount
Int — Default: 4
Equivalent to FilterMutectCalls' `--unique-alt-read-count` option.
Mutect2.gatherVcfs.compressionLevel
Int — Default: 1
The compression level at which the BAM files are written.
Mutect2.gatherVcfs.javaXmx
String — Default: "4G"
The maximum memory available to the program. Should be lower than `memory` to accommodate JVM overhead.
Mutect2.gatherVcfs.memory
String — Default: "5G"
The amount of memory this job will use.
Mutect2.gatherVcfs.timeMinutes
Int — Default: 1 + ceil(size(inputVCFs,"G")) * 2
The maximum amount of time the job will run in minutes.
Mutect2.gatherVcfs.useJdkDeflater
Boolean — Default: true
True, uses the java deflator to compress the BAM files. False uses the optimized intel deflater.
Mutect2.gatherVcfs.useJdkInflater
Boolean — Default: true
True, uses the java inflater. False, uses the optimized intel inflater.
Mutect2.getPileupSummariesNormal.javaXmx
String — Default: "12G"
The maximum memory available to the program. Should be lower than `memory` to accommodate JVM overhead.
Mutect2.getPileupSummariesNormal.memory
String — Default: "13G"
The amount of memory this job will use.
Mutect2.getPileupSummariesNormal.timeMinutes
Int — Default: 120
The maximum amount of time the job will run in minutes.
Mutect2.getPileupSummariesTumor.javaXmx
String — Default: "12G"
The maximum memory available to the program. Should be lower than `memory` to accommodate JVM overhead.
Mutect2.getPileupSummariesTumor.memory
String — Default: "13G"
The amount of memory this job will use.
Mutect2.getPileupSummariesTumor.timeMinutes
Int — Default: 120
The maximum amount of time the job will run in minutes.
Mutect2.learnReadOrientationModel.javaXmx
String — Default: "12G"
The maximum memory available to the program. Should be lower than `memory` to accommodate JVM overhead.
Mutect2.learnReadOrientationModel.memory
String — Default: "13G"
The amount of memory this job will use.
Mutect2.learnReadOrientationModel.timeMinutes
Int — Default: 120
The maximum amount of time the job will run in minutes.
Mutect2.mergeStats.javaXmx
String — Default: "14G"
The maximum memory available to the program. Should be lower than `memory` to accommodate JVM overhead.
Mutect2.mergeStats.memory
String — Default: "15G"
The amount of memory this job will use.
Mutect2.mergeStats.timeMinutes
Int — Default: 30
The maximum amount of time the job will run in minutes.
Mutect2.mutect2.f1r2TarGz
String — Default: "f1r2.tar.gz"
Equivalent to Mutect2's `--f1r2-tar-gz` option.
Mutect2.mutect2.germlineResource
File?
Equivalent to Mutect2's `--germline-resource` option.
Mutect2.mutect2.germlineResourceIndex
File?
The index for the germline resource.
Mutect2.mutect2.javaXmx
String — Default: "4G"
The maximum memory available to the program. Should be lower than `memory` to accommodate JVM overhead.
Mutect2.mutect2.memory
String — Default: "5G"
The amount of memory this job will use.
Mutect2.mutect2.outputStats
String — Default: outputVcf + ".stats"
The location the output statistics should be written to.
Mutect2.mutect2.panelOfNormals
File?
Equivalent to Mutect2's `--panel-of-normals` option.
Mutect2.mutect2.panelOfNormalsIndex
File?
The index for the panel of normals.
Mutect2.mutect2.timeMinutes
Int — Default: 240
The maximum amount of time the job will run in minutes.
Mutect2.scatterList.memory
String — Default: "256M"
The amount of memory this job will use.
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>
Mutect2.scatterList.timeMinutes
Int — Default: 2
The maximum amount of time the job will run in minutes.
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.
Mutect2.scatterSizeMillions
Int — Default: 1000
Same as scatterSize, but is multiplied by 1000000 to get scatterSize. This allows for setting larger values more easily
Mutect2.sitesForContamination
File?
A bed file, vcf file or interval list with regions for GetPileupSummaries to operate on.
Mutect2.sitesForContaminationIndex
File?
The index for the vcf file provided to sitesForContamination.
Mutect2.variantsForContamination
File?
A VCF file with common variants.
Mutect2.variantsForContaminationIndex
File?
The index of the common variants VCF file.
</dl> </details>