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