Performs local realignment around indels to correct for mapping errors
meta{:bash}
:map
Groovy Map containing sample information e.g. [ id:‘test’, single_end:false ]
bam{:bash}
:file
Sorted and indexed BAM file
*.bam
bai{:bash}
BAM index file
*.bai
intervals{:bash}
Intervals file created by gatk3 RealignerTargetCreator
*.{intervals,list}
meta2{:bash}
Groovy Map containing reference information. e.g. [ id:‘test’, single_end:false ]
fasta{:bash}
Reference file used to generate BAM file
.{fasta,fa,fna}
meta3{:bash}
fai{:bash}
Index of reference file used to generate BAM file
.fai
meta4{:bash}
dict{:bash}
GATK dict file for reference
.dict
meta5{:bash}
Groovy Map containing file meta-information for known_vcf. e.g. [ id:‘test’, single_end:false ]
known_vcf{:bash}
Optional input VCF file(s) with known indels
.vcf
*.bam{:bash}
Sorted and indexed BAM file with local realignment around variants
*.bai{:bash}
versions{:bash}
versions.yml{:bash}
File containing software versions
versions.yml
The full Genome Analysis Toolkit (GATK) framework, license restricted.
