SNP and Indel variant caller on a per-locus basis
meta
:map
Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]
bam
:file
Sorted and indexed BAM/CRAM/SAM file
*.bam
bai
BAM index file
*.bai
meta2
Groovy Map containing reference information. e.g. [ id:‘test’, single_end:false ]
fasta
Reference file used to generate BAM file
.{fasta,fa,fna}
meta3
fai
Index of reference file used to generate BAM file
.fai
meta4
dict
GATK dict file for reference
.dict
meta5
intervals
Bed file with the genomic regions included in the library (optional)
*.intervals
meta6
Groovy Map containing file meta-information for the contamination file. e.g. [ id:‘test’, single_end:false ]
contamination
Tab-separated file containing fraction of contamination in sequencing data (per sample) to aggressively remove
*
meta7
Groovy Map containing file meta-information for the dbsnps file. e.g. [ id:‘test’, single_end:false ]
dbsnp
VCF file containing known sites (optional)
meta8
Groovy Map containing file meta-information for the VCF comparison file. e.g. [ id:‘test’, single_end:false ]
comp
Comparison VCF file (optional)
vcf
*.vcf.gz
VCF file containing called variants
versions_gatk
${task.process}
:string
The name of the process
gatk
The name of the tool
gatk3 --version
:eval
The expression to obtain the version of the tool
versions
The full Genome Analysis Toolkit (GATK) framework, license restricted.
