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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:
"24G"
The amount of memory this job will use. - Mutect2.dockerImages
-
Map[String,String] — Default:
{"picard": "quay.io/biocontainers/picard:2.19.0--0", "gatk4": "quay.io/biocontainers/gatk4:4.1.2.0--1", "biopet-scatterregions": "quay.io/biocontainers/biopet-scatterregions:0.2--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:
"24G"
The amount of memory this job will use. - Mutect2.filterMutectCalls.uniqueAltReadCount
-
Int — Default:
4
Equivalent to FilterMutectCalls' `--unique-alt-read-count` option. - Mutect2.gatherVcfs.javaXmx
-
String — Default:
"8G"
The maximum memory available to the program. Should be lower than `memory` to accommodate JVM overhead. - Mutect2.gatherVcfs.memory
-
String — Default:
"24G"
The amount of memory this job will use. - 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:
"24G"
The amount of memory this job will use. - 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:
"24G"
The amount of memory this job will use. - 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:
"24G"
The amount of memory this job will use. - 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:
"28G"
The amount of memory this job will use. - 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:
"16G"
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.scatterList.bamFile
-
File?
Equivalent to biopet scatterregions' `--bamfile` option. - Mutect2.scatterList.bamIndex
-
File?
The index for the bamfile given through bamFile. - Mutect2.scatterList.javaXmx
-
String — Default:
"8G"
The maximum memory available to the program. Should be lower than `memory` to accommodate JVM overhead. - Mutect2.scatterList.memory
-
String — Default:
"24G"
The amount of memory this job will use. - Mutect2.scatterSize
-
Int — Default:
1000000000
The size of the scattered regions in bases. Scattering is used to speed up certain processes. The genome will be sseperated 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.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.