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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:
"24G"
The amount of memory this job will use. - SomaticVariantcalling.dockerImages
-
Map[String,String] — Default:
{"picard": "quay.io/biocontainers/picard:2.19.0--0", "biopet-scatterregions": "quay.io/biocontainers/biopet-scatterregions:0.2--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", "gatk4": "quay.io/biocontainers/gatk4:4.1.2.0--1", "vardict-java": "quay.io/biocontainers/vardict-java:1.5.8--1", "somaticseq": "lethalfang/somaticseq:3.1.0"}
The docker images used. Changing this may result in errors which the developers may choose not to address. - 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:
"24G"
The amount of memory this job will use. - 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:
"24G"
The amount of memory this job will use. - SomaticVariantcalling.mutect2.filterMutectCalls.uniqueAltReadCount
-
Int — Default:
4
Equivalent to FilterMutectCalls' `--unique-alt-read-count` option. - SomaticVariantcalling.mutect2.gatherVcfs.javaXmx
-
String — Default:
"8G"
The maximum memory available to the program. Should be lower than `memory` to accommodate JVM overhead. - SomaticVariantcalling.mutect2.gatherVcfs.memory
-
String — Default:
"24G"
The amount of memory this job will use. - 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:
"24G"
The amount of memory this job will use. - 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:
"24G"
The amount of memory this job will use. - 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:
"24G"
The amount of memory this job will use. - 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:
"28G"
The amount of memory this job will use. - 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:
"16G"
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.scatterList.bamFile
-
File?
Equivalent to biopet scatterregions' `--bamfile` option. - SomaticVariantcalling.mutect2.scatterList.bamIndex
-
File?
The index for the bamfile given through bamFile. - SomaticVariantcalling.mutect2.scatterList.javaXmx
-
String — Default:
"8G"
The maximum memory available to the program. Should be lower than `memory` to accommodate JVM overhead. - SomaticVariantcalling.mutect2.scatterList.memory
-
String — Default:
"24G"
The amount of memory this job will use. - SomaticVariantcalling.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. - 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.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.varscanIndel
-
File?
An indel VCF as produced by varscan. - SomaticVariantcalling.pairedSomaticSeq.varscanSNV
-
File?
An SNV VCF as produced by varscan. - SomaticVariantcalling.pairedTraining.threads
-
Int — Default:
1
The number of threads to use. - 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.scalpelVCF
-
File?
A VCF as produced by scalpel. - SomaticVariantcalling.singleSomaticSeq.threads
-
Int — Default:
1
The number of threads to use. - SomaticVariantcalling.singleSomaticSeq.varscanVCF
-
File?
A VCF as produced by varscan. - SomaticVariantcalling.singleTraining.threads
-
Int — Default:
1
The number of threads to use. - 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.strelka.addGTFieldIndels.outputVCFName
-
String — Default:
basename(strelkaVCF,".gz")
The location the output VCF file should be written to. - SomaticVariantcalling.strelka.addGTFieldSVs.outputVCFName
-
String — Default:
basename(strelkaVCF,".gz")
The location the output VCF file should be written to. - SomaticVariantcalling.strelka.addGTFieldVariants.outputVCFName
-
String — Default:
basename(strelkaVCF,".gz")
The location the output VCF file should be written to. - 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:
"24G"
The amount of memory this job will use. - SomaticVariantcalling.strelka.gatherIndels.javaXmx
-
String — Default:
"8G"
The maximum memory available to the program. Should be lower than `memory` to accommodate JVM overhead. - SomaticVariantcalling.strelka.gatherIndels.memory
-
String — Default:
"24G"
The amount of memory this job will use. - SomaticVariantcalling.strelka.gatherSVs.javaXmx
-
String — Default:
"8G"
The maximum memory available to the program. Should be lower than `memory` to accommodate JVM overhead. - SomaticVariantcalling.strelka.gatherSVs.memory
-
String — Default:
"24G"
The amount of memory this job will use. - SomaticVariantcalling.strelka.gatherVariants.javaXmx
-
String — Default:
"8G"
The maximum memory available to the program. Should be lower than `memory` to accommodate JVM overhead. - SomaticVariantcalling.strelka.gatherVariants.memory
-
String — Default:
"24G"
The amount of memory this job will use. - 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.scatterList.bamFile
-
File?
Equivalent to biopet scatterregions' `--bamfile` option. - SomaticVariantcalling.strelka.scatterList.bamIndex
-
File?
The index for the bamfile given through bamFile. - SomaticVariantcalling.strelka.scatterList.javaXmx
-
String — Default:
"8G"
The maximum memory available to the program. Should be lower than `memory` to accommodate JVM overhead. - SomaticVariantcalling.strelka.scatterList.memory
-
String — Default:
"24G"
The amount of memory this job will use. - SomaticVariantcalling.strelka.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. - 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.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.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.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.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:
"24G"
The amount of memory this job will use. - SomaticVariantcalling.vardict.scatterList.chunkSize
-
Int?
Equivalent to chunked-scatter's `-c` option. - SomaticVariantcalling.vardict.scatterList.dockerImage
-
String — Default:
"quay.io/biocontainers/chunked-scatter:0.1.0--py_0"
The docker image used for this task. Changing this may result in errors which the developers may choose not to address. - 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.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:
"40G"
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.variantsForContamination
-
File?
A VCF file with common variants. - SomaticVariantcalling.variantsForContaminationIndex
-
File?
The index of the common variants VCF file.
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