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Inputs for GatkVariantCalling
The following is an overview of all available inputs in GatkVariantCalling.
Required inputs
- GatkVariantCalling.bamFiles
-
Array[struct(file : File, index : File, md5sum : String?)] — Default:
None
BAM files to be analysed by GATK. The should be recalibrated beforehand if required. - GatkVariantCalling.dbsnpVCF
-
File — Default:
None
dbsnp VCF file used for checking known sites - GatkVariantCalling.dbsnpVCFIndex
-
File — Default:
None
index (.tbi) file for the dbsnp VCF - GatkVariantCalling.referenceFasta
-
File — Default:
None
The reference fasta file - GatkVariantCalling.referenceFastaDict
-
File — Default:
None
Sequence dictionary (.dict) file of the reference - GatkVariantCalling.referenceFastaFai
-
File — Default:
None
Fasta index (.fai) file of the reference
Other common inputs
- GatkVariantCalling.outputDir
-
String — Default:
"."
The directory where the output files should be located - GatkVariantCalling.vcfBasename
-
String — Default:
"multisample"
The basename of the VCF and GVCF files that are outputted by the workflow
Advanced inputs
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- GatkVariantCalling.dockerImages
-
Map[String,String] — Default:
{"picard": "quay.io/biocontainers/picard:2.20.5--0", "gatk4": "quay.io/biocontainers/gatk4:4.1.0.0--0", "biopet-scatterregions": "quay.io/biocontainers/biopet-scatterregions:0.2--0"}
specify which docker images should be used for running this pipeline
Other inputs
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- GatkVariantCalling.gatherGvcfs.intervals
-
Array[File] — Default:
[]
??? - GatkVariantCalling.gatherGvcfs.javaXmx
-
String — Default:
"12G"
??? - GatkVariantCalling.gatherGvcfs.memory
-
String — Default:
"24G"
??? - GatkVariantCalling.gatherVcfs.javaXmx
-
String — Default:
"8G"
??? - GatkVariantCalling.gatherVcfs.memory
-
String — Default:
"24G"
??? - GatkVariantCalling.genotypeGvcfs.javaXmx
-
String — Default:
"6G"
??? - GatkVariantCalling.genotypeGvcfs.memory
-
String — Default:
"18G"
??? - GatkVariantCalling.Gvcf.haplotypeCallerGvcf.contamination
-
Float — Default:
0.0
??? - GatkVariantCalling.Gvcf.haplotypeCallerGvcf.javaXmx
-
String — Default:
"4G"
??? - GatkVariantCalling.Gvcf.haplotypeCallerGvcf.memory
-
String — Default:
"12G"
??? - GatkVariantCalling.orderedScatters.dockerImage
-
String — Default:
"python:3.7-slim"
??? - GatkVariantCalling.regions
-
File? — Default:
None
??? - GatkVariantCalling.scatterList.bamFile
-
File? — Default:
None
??? - GatkVariantCalling.scatterList.bamIndex
-
File? — Default:
None
??? - GatkVariantCalling.scatterList.javaXmx
-
String — Default:
"8G"
??? - GatkVariantCalling.scatterList.memory
-
String — Default:
"24G"
??? - GatkVariantCalling.scatterList.notSplitContigs
-
Boolean — Default:
false
??? - GatkVariantCalling.scatterSize
-
Int — Default:
1000000000
???