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Inputs for Strelka
The following is an overview of all available inputs in Strelka.
Required inputs
- Strelka.referenceFasta
-
File
The reference fasta file. - Strelka.referenceFastaDict
-
File
Sequence dictionary (.dict) file of the reference. - Strelka.referenceFastaFai
-
File
Fasta index (.fai) file of the reference. - Strelka.tumorBam
-
File
The BAM file for the tumor/case sample. - Strelka.tumorBamIndex
-
File
The index for the tumor/case sample's BAM file.
Other common inputs
- Strelka.basename
-
String — Default:
"strelka"
The basename for the output. - Strelka.controlBam
-
File?
The BAM file for the normal/control sample. - Strelka.controlBamIndex
-
File?
The index for the normal/control sample's BAM file. - Strelka.exome
-
Boolean — Default:
false
Whether or not the data is from exome sequencing. - Strelka.outputDir
-
String — Default:
"."
The directory to which the outputs will be written. - Strelka.regions
-
File?
A bed file describing the regions to operate on. - Strelka.rna
-
Boolean — Default:
false
Whether or not the data is from RNA sequencing. - Strelka.runManta
-
Boolean — Default:
true
Whether or not manta should be run.
Advanced inputs
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- Strelka.addGTFieldIndels.outputVCFName
-
String — Default:
basename(strelkaVCF,".gz")
The location the output VCF file should be written to. - Strelka.addGTFieldSVs.outputVCFName
-
String — Default:
basename(strelkaVCF,".gz")
The location the output VCF file should be written to. - Strelka.addGTFieldVariants.outputVCFName
-
String — Default:
basename(strelkaVCF,".gz")
The location the output VCF file should be written to. - 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. - Strelka.combineVariants.filteredRecordsMergeType
-
String — Default:
"KEEP_IF_ANY_UNFILTERED"
Equivalent to CombineVariants' `--filteredrecordsmergetype` option. - Strelka.combineVariants.genotypeMergeOption
-
String — Default:
"UNIQUIFY"
Equivalent to CombineVariants' `--genotypemergeoption` option. - Strelka.combineVariants.javaXmx
-
String — Default:
"12G"
The maximum memory available to the program. Should be lower than `memory` to accommodate JVM overhead. - Strelka.combineVariants.memory
-
String — Default:
"24G"
The amount of memory this job will use. - Strelka.dockerImages
-
Map[String,String] — Default:
{"picard": "quay.io/biocontainers/picard:2.18.26--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", "somaticseq": "lethalfang/somaticseq:3.1.0"}
The docker images used. Changing this may result in errors which the developers may choose not to address. - Strelka.gatherIndels.javaXmx
-
String — Default:
"8G"
The maximum memory available to the program. Should be lower than `memory` to accommodate JVM overhead. - Strelka.gatherIndels.memory
-
String — Default:
"24G"
The amount of memory this job will use. - Strelka.gatherSVs.javaXmx
-
String — Default:
"8G"
The maximum memory available to the program. Should be lower than `memory` to accommodate JVM overhead. - Strelka.gatherSVs.memory
-
String — Default:
"24G"
The amount of memory this job will use. - Strelka.gatherVariants.javaXmx
-
String — Default:
"8G"
The maximum memory available to the program. Should be lower than `memory` to accommodate JVM overhead. - Strelka.gatherVariants.memory
-
String — Default:
"24G"
The amount of memory this job will use. - Strelka.mantaSomatic.cores
-
Int — Default:
1
The number of cores to use. - Strelka.mantaSomatic.memoryGb
-
Int — Default:
4
The amount of memory this job will use in Gigabytes. - Strelka.runCombineVariants
-
Boolean — Default:
false
Whether or not found variants should be combined into a single VCf file. - Strelka.scatterList.bamFile
-
File?
Equivalent to biopet scatterregions' `--bamfile` option. - Strelka.scatterList.bamIndex
-
File?
The index for the bamfile given through bamFile. - Strelka.scatterList.javaXmx
-
String — Default:
"8G"
The maximum memory available to the program. Should be lower than `memory` to accommodate JVM overhead. - Strelka.scatterList.memory
-
String — Default:
"24G"
The amount of memory this job will use. - 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. - Strelka.strelkaGermline.cores
-
Int — Default:
1
The number of cores to use. - Strelka.strelkaGermline.memoryGb
-
Int — Default:
4
The amount of memory this job will use in Gigabytes. - Strelka.strelkaSomatic.cores
-
Int — Default:
1
The number of cores to use. - Strelka.strelkaSomatic.memoryGb
-
Int — Default:
4
The amount of memory this job will use in Gigabytes.
Do not set these inputs!
The following inputs should not be set, even though womtool may show them as being available inputs.
- Strelka.indelsIndex.type
- Strelka.svsIndex.type
- Strelka.variantsIndex.type
- Strelka.strelkaSomatic.doNotDefineThis