This is not a stable version!
You are currently viewing the documentation for a development version. It is not guaranteed that this documentation is up to date. Things will likely change without announcement or versioning incrementation. If there is no other documentation available, there are likely no releases available for this repository. The content is, therefore, likely still in development and not production ready. Use at your own risk!
Please be aware that the page you are currently viewing is not for the latest available version!
Inputs for GatkPreprocess
The following is an overview of all available inputs in GatkPreprocess.
Required inputs
- GatkPreprocess.bam
-
File
The BAM file which should be processed - GatkPreprocess.bamIndex
-
File
The index for the BAM file - GatkPreprocess.dbsnpVCF
-
File
A dbSNP vcf. - GatkPreprocess.dbsnpVCFIndex
-
File
Index for dbSNP vcf. - GatkPreprocess.referenceFasta
-
File
The reference fasta file - GatkPreprocess.referenceFastaDict
-
File
Sequence dictionary (.dict) for the reference fasta file - GatkPreprocess.referenceFastaFai
-
File
Fasta index (.fai) for the reference fasta file - GatkPreprocess.scatters
-
Array[File]
The bed files to be used
Other common inputs
- GatkPreprocess.bamName
-
String — Default:
"recalibrated"
The basename for the produced BAM files. This should not include any parent direcoties, use `outputDir` if the output directory should be changed. - GatkPreprocess.outputDir
-
String — Default:
"."
The directory to which the outputs will be written. - GatkPreprocess.splitSplicedReads
-
Boolean — Default:
false
Whether or not gatk's SplitNCgarReads should be run to split spliced reads. This should be enabled for RNAseq samples.
Advanced inputs
Show/Hide
- GatkPreprocess.applyBqsr.javaXmxMb
-
Int — Default:
2048
The maximum memory available to the program in megabytes. Should be lower than `memoryMb` to accommodate JVM overhead. - GatkPreprocess.applyBqsr.memoryMb
-
Int — Default:
javaXmxMb + 512
The amount of memory this job will use in megabytes. - GatkPreprocess.baseRecalibrator.javaXmxMb
-
Int — Default:
1024
The maximum memory available to the program in megabytes. Should be lower than `memoryMb` to accommodate JVM overhead. - GatkPreprocess.baseRecalibrator.knownIndelsSitesVCFIndexes
-
Array[File] — Default:
[]
The indexed for the known variant VCFs. - GatkPreprocess.baseRecalibrator.knownIndelsSitesVCFs
-
Array[File] — Default:
[]
VCF files with known indels. - GatkPreprocess.baseRecalibrator.memoryMb
-
Int — Default:
javaXmxMb + 512
The amount of memory this job will use in megabytes. - GatkPreprocess.dockerImages
-
Map[String,String] — Default:
{"picard": "quay.io/biocontainers/picard:2.23.2--0", "gatk4": "quay.io/biocontainers/gatk4:4.1.8.0--py38h37ae868_0"}
The docker images used. Changing this may result in errors which the developers may choose not to address. - GatkPreprocess.gatherBamFiles.compressionLevel
-
Int?
The compression level of the output BAM. - GatkPreprocess.gatherBamFiles.createMd5File
-
Boolean — Default:
false
??? - GatkPreprocess.gatherBamFiles.javaXmxMb
-
Int — Default:
1024
The maximum memory available to the program in megabytes. Should be lower than `memoryMb` to accommodate JVM overhead. - GatkPreprocess.gatherBamFiles.memoryMb
-
Int — Default:
javaXmxMb + 512
The amount of memory this job will use in megabytes. - GatkPreprocess.gatherBamFiles.timeMinutes
-
Int — Default:
1 + ceil((size(inputBams,"G") * 1))
The maximum amount of time the job will run in minutes. - GatkPreprocess.gatherBqsr.javaXmxMb
-
Int — Default:
256
The maximum memory available to the program in megabytes. Should be lower than `memory` to accommodate JVM overhead. - GatkPreprocess.gatherBqsr.memoryMb
-
Int — Default:
256 + javaXmxMb
The amount of memory this job will use in megabytes. - GatkPreprocess.gatherBqsr.timeMinutes
-
Int — Default:
1
The maximum amount of time the job will run in minutes. - GatkPreprocess.splitNCigarReads.javaXmx
-
String — Default:
"4G"
The maximum memory available to the program. Should be lower than `memory` to accommodate JVM overhead. - GatkPreprocess.splitNCigarReads.memory
-
String — Default:
"5G"
The amount of memory this job will use.