name: "gatk_realignertargetcreator" description: Generates a list of locations that should be considered for local realignment prior genotyping. keywords: - bam - vcf - variant calling - indel - realignment - targets tools: - "gatk": description: "The full Genome Analysis Toolkit (GATK) framework, license restricted." homepage: "https://gatk.broadinstitute.org/hc/en-us" documentation: "https://github.com/broadinstitute/gatk-docs" licence: "['https://software.broadinstitute.org/gatk/download/licensing', 'BSD', 'https://www.broadinstitute.org/gatk/about/#licensing']" input: - meta: type: map description: | Groovy Map containing sample information e.g. [ id:'test', single_end:false ] - input: type: file description: Sorted and indexed BAM/CRAM/SAM file pattern: "*.bam" - index: type: file description: BAM index file pattern: "*.bai" - fasta: type: file description: Reference file used to generate BAM file pattern: ".{fasta,fa,fna}" - fai: type: file description: Index of reference file used to generate BAM file pattern: ".fai" - dict: type: file description: GATK dict file for reference pattern: ".dict" - known_vcf: type: file description: Optional input VCF file(s) with known indels pattern: ".vcf" output: - meta: type: map description: | Groovy Map containing sample information e.g. [ id:'test', single_end:false ] - versions: type: file description: File containing software versions pattern: "versions.yml" - intervals: type: file description: File containg intervals that represent sites of extant and potential indels. pattern: "*.intervals" authors: - "@jfy133"