BioWDL: somatic-variantcalling

A pipeline for somatic variantcalling.

Inputs for VarDict

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

Required inputs

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

Other common inputs

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

Advanced inputs

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VarDict.dockerImages
Map[String,String] — Default: {"picard": "quay.io/biocontainers/picard:2.23.2--0", "vardict-java": "quay.io/biocontainers/vardict-java:1.5.8--1", "samtools": "quay.io/biocontainers/samtools:1.10--h9402c20_2", "chunked-scatter": "quay.io/biocontainers/chunked-scatter:0.2.0--py_0"}
The docker images used. Changing this may result in errors which the developers may choose not to address.
VarDict.filterSupplementaryAlignments
Boolean — Default: false
Whether or not supplementary reads should be filtered before vardict is run.
VarDict.filterSupplementaryControl.excludeSpecificFilter
Int?
Equivalent to samtools view's `-G` option.
VarDict.filterSupplementaryControl.includeFilter
Int?
Equivalent to samtools view's `-f` option.
VarDict.filterSupplementaryControl.MAPQthreshold
Int?
Equivalent to samtools view's `-q` option.
VarDict.filterSupplementaryControl.memory
String — Default: "1G"
The amount of memory this job will use.
VarDict.filterSupplementaryControl.referenceFasta
File?
The reference fasta file also used for mapping.
VarDict.filterSupplementaryControl.threads
Int — Default: 1
The number of threads to use.
VarDict.filterSupplementaryControl.timeMinutes
Int — Default: 1 + ceil((size(inFile,"G") * 5))
The maximum amount of time the job will run in minutes.
VarDict.filterSupplementaryControl.uncompressedBamOutput
Boolean — Default: false
Equivalent to samtools view's `-u` flag.
VarDict.filterSupplementaryTumor.excludeSpecificFilter
Int?
Equivalent to samtools view's `-G` option.
VarDict.filterSupplementaryTumor.includeFilter
Int?
Equivalent to samtools view's `-f` option.
VarDict.filterSupplementaryTumor.MAPQthreshold
Int?
Equivalent to samtools view's `-q` option.
VarDict.filterSupplementaryTumor.memory
String — Default: "1G"
The amount of memory this job will use.
VarDict.filterSupplementaryTumor.referenceFasta
File?
The reference fasta file also used for mapping.
VarDict.filterSupplementaryTumor.threads
Int — Default: 1
The number of threads to use.
VarDict.filterSupplementaryTumor.timeMinutes
Int — Default: 1 + ceil((size(inFile,"G") * 5))
The maximum amount of time the job will run in minutes.
VarDict.filterSupplementaryTumor.uncompressedBamOutput
Boolean — Default: false
Equivalent to samtools view's `-u` flag.
VarDict.gatherVcfs.javaXmx
String — Default: "8G"
The maximum memory available to the program. Should be lower than `memory` to accommodate JVM overhead.
VarDict.gatherVcfs.memory
String — Default: "9G"
The amount of memory this job will use.
VarDict.gatherVcfs.timeMinutes
Int — Default: 1 + ceil((size(vcfFiles,"G") * 5))
The maximum amount of time the job will run in minutes.
VarDict.scatterList.chunkSize
Int?
Equivalent to chunked-scatter's `-c` option.
VarDict.scatterList.memory
String — Default: "256M"
The amount of memory this job will use.
VarDict.scatterList.minimumBasesPerFile
Int?
Equivalent to chunked-scatter's `-m` option.
VarDict.scatterList.overlap
Int?
Equivalent to chunked-scatter's `-o` option.
VarDict.scatterList.prefix
String — Default: "./scatter"
The prefix for the output files.
VarDict.scatterList.splitContigs
Boolean — Default: false
If set, contigs are allowed to be split up over multiple files.
VarDict.scatterList.timeMinutes
Int — Default: 2
The maximum amount of time the job will run in minutes.
VarDict.varDict.chromosomeColumn
Int — Default: 1
Equivalent to vardict-java's `-c` option.
VarDict.varDict.endColumn
Int — Default: 3
Equivalent to vardict-java's `-E` option.
VarDict.varDict.geneColumn
Int — Default: 4
Equivalent to vardict-java's `-g` option.
VarDict.varDict.javaXmx
String — Default: "16G"
The maximum memory available to the program. Should be lower than `memory` to accommodate JVM overhead.
VarDict.varDict.mappingQuality
Float — Default: 20
Equivalent to var2vcf_paired.pl or var2vcf_valid.pl's `-Q` option.
VarDict.varDict.memory
String — Default: "18G"
The amount of memory this job will use.
VarDict.varDict.minimumAlleleFrequency
Float — Default: 0.02
Equivalent to var2vcf_paired.pl or var2vcf_valid.pl's `-f` option.
VarDict.varDict.minimumTotalDepth
Int — Default: 8
Equivalent to var2vcf_paired.pl or var2vcf_valid.pl's `-d` option.
VarDict.varDict.minimumVariantDepth
Int — Default: 4
Equivalent to var2vcf_paired.pl or var2vcf_valid.pl's `-v` option.
VarDict.varDict.outputAllVariantsAtSamePosition
Boolean — Default: true
Equivalent to var2vcf_paired.pl or var2vcf_valid.pl's `-A` flag.
VarDict.varDict.outputCandidateSomaticOnly
Boolean — Default: true
Equivalent to var2vcf_paired.pl or var2vcf_valid.pl's `-M` flag.
VarDict.varDict.startColumn
Int — Default: 2
Equivalent to vardict-java's `-S` option.
VarDict.varDict.threads
Int — Default: 1
The number of threads to use.
VarDict.varDict.timeMinutes
Int — Default: 300
The maximum amount of time the job will run in minutes.