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