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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.