name: "bcftools_roh" description: A program for detecting runs of homo/autozygosity. Only bi-allelic sites are considered. keywords: - roh tools: - "roh": description: "A program for detecting runs of homo/autozygosity. Only bi-allelic sites are considered." homepage: https://www.htslib.org/ documentation: http://www.htslib.org/doc/bcftools.html doi: 10.1093/bioinformatics/btp352 licence: ["MIT"] input: - meta: type: map description: | Groovy Map containing sample information e.g. [ id:'test', single_end:false ] - vcf: type: file description: VCF file pattern: "*.{vcf,.vcf.gz}" - af_file: type: file description: "Read allele frequencies from a tab-delimited file containing the columns: CHROM\tPOS\tREF,ALT\tAF." - genetic_map: type: file description: "Genetic map in the format required also by IMPUTE2." - regions_file: type: file description: "Regions can be specified either on command line or in a VCF, BED, or tab-delimited file (the default)." - samples_file: type: file description: "File of sample names to include or exclude if prefixed with '^'." - targets_file: type: file description: "Targets can be specified either on command line or in a VCF, BED, or tab-delimited file (the default)." 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" - roh: type: file description: Contains site-specific and/or per-region runs of homo/autozygosity calls. pattern: "*.{roh}" authors: - "@ramprasadn"