name: vcftools description: A set of tools written in Perl and C++ for working with VCF files keywords: VCF - sort tools: - vcftools: description: A set of tools written in Perl and C++ for working with VCF files. This package only contains the C++ libraries whereas the package perl-vcftools-vcf contains the perl libraries homepage: http://vcftools.sourceforge.net/ documentation: http://vcftools.sourceforge.net/man_latest.html tool_dev_url: None doi: licence: ['LGPL'] input: - meta: type: map description: | Groovy Map containing sample information e.g. [ id:'test', single_end:false ] - variant_file: type: file description: variant input file which can be vcf, vcf.gz, or bcf format. - bed: type: file description: bed file which can be used with different arguments in vcftools (optional) - diff_variant_file: type: file description: secondary variant file which can be used with the 'diff' suite of tools (optional) output: - meta: type: map description: | Groovy Map containing sample information e.g. [ id:'test', single_end:false ] - version: type: file description: File containing software version pattern: "versions.yml" - vcf: type: file description: vcf file (optional) pattern: "*.vcf" - bcf: type: file description: bcf file (optional) pattern: "*.bcf" - frq: type: file description: Allele frequency for each site (optional) pattern: "*.frq" - frq_count: type: file description: Allele counts for each site (optional) pattern: "*.frq.count" - idepth: type: file description: mean depth per individual (optional) pattern: "*.idepth" - ldepth: type: file description: depth per site summed across individuals (optional) pattern: "*.ildepth" - ldepth_mean: type: file description: mean depth per site calculated across individuals (optional) pattern: "*.ldepth.mean" - gdepth: type: file description: depth for each genotype in vcf file (optional) pattern: "*.gdepth" - hap_ld: type: file description: r2, D, and D’ statistics using phased haplotypes (optional) pattern: "*.hap.ld" - geno_ld: type: file description: squared correlation coefficient between genotypes encoded as 0, 1 and 2 to represent the number of non-reference alleles in each individual (optional) pattern: "*.geno.ld" - geno_chisq: type: file description: test for genotype independence via the chi-squared statistic (optional) pattern: "*.geno.chisq" - list_hap_ld: type: file description: r2 statistics of the sites contained in the provided input file verses all other sites (optional) pattern: "*.list.hap.ld" - list_geno_ld: type: file description: r2 statistics of the sites contained in the provided input file verses all other sites (optional) pattern: "*.list.geno.ld" - interchrom_hap_ld: type: file description: r2 statistics for sites (haplotypes) on different chromosomes (optional) pattern: "*.interchrom.hap.ld" - interchrom_geno_ld: type: file description: r2 statistics for sites (genotypes) on different chromosomes (optional) pattern: "*.interchrom.geno.ld" - tstv: type: file description: Transition / Transversion ratio in bins of size defined in options (optional) pattern: "*.TsTv" - tstv_summary: type: file description: Summary of all Transitions and Transversions (optional) pattern: "*.TsTv.summary" - tstv_count: type: file description: Transition / Transversion ratio as a function of alternative allele count (optional) pattern: "*.TsTv.count" - tstv_qual: type: file description: Transition / Transversion ratio as a function of SNP quality threshold (optional) pattern: "*.TsTv.qual" - filter_summary: type: file description: Summary of the number of SNPs and Ts/Tv ratio for each FILTER category (optional) pattern: "*.FILTER.summary" - sites_pi: type: file description: Nucleotide divergency on a per-site basis (optional) pattern: "*.sites.pi" - windowed_pi: type: file description: Nucleotide diversity in windows, with window size determined by options (optional) pattern: "*windowed.pi" - weir_fst: type: file description: Fst estimate from Weir and Cockerham’s 1984 paper (optional) pattern: "*.weir.fst" - heterozygosity: type: file description: Heterozygosity on a per-individual basis (optional) pattern: "*.het" - hwe: type: file description: Contains the Observed numbers of Homozygotes and Heterozygotes and the corresponding Expected numbers under HWE (optional) pattern: "*.hwe" - tajima_d: type: file description: Tajima’s D statistic in bins with size of the specified number in options (optional) pattern: "*.Tajima.D" - freq_burden: type: file description: Number of variants within each individual of a specific frequency in options (optional) pattern: "*.ifreqburden" - lroh: type: file description: Long Runs of Homozygosity (optional) pattern: "*.LROH" - relatedness: type: file description: Relatedness statistic based on the method of Yang et al, Nature Genetics 2010 (doi:10.1038/ng.608) (optional) pattern: "*.relatedness" - relatedness2: type: file description: Relatedness statistic based on the method of Manichaikul et al., BIOINFORMATICS 2010 (doi:10.1093/bioinformatics/btq559) (optional) pattern: "*.relatedness2" - lqual: type: file description: per-site SNP quality (optional) pattern: "*.lqual" - missing_individual: type: file description: Missingness on a per-individual basis (optional) pattern: "*.imiss" - missing_site: type: file description: Missingness on a per-site basis (optional) pattern: "*.lmiss" - snp_density: type: file description: Number and density of SNPs in bins of size defined by option (optional) pattern: "*.snpden" - kept_sites: type: file description: All sites that have been kept after filtering (optional) pattern: "*.kept.sites" - removed_sites: type: file description: All sites that have been removed after filtering (optional) pattern: "*.removed.sites" - singeltons: type: file description: Location of singletons, and the individual they occur in (optional) pattern: "*.singeltons" - indel_hist: type: file description: Histogram file of the length of all indels (including SNPs) (optional) pattern: "*.indel_hist" - hapcount: type: file description: Unique haplotypes within user specified bins (optional) pattern: "*.hapcount" - mendel: type: file description: Mendel errors identified in trios (optional) pattern: "*.mendel" - format: type: file description: Extracted information from the genotype fields in the VCF file relating to a specfied FORMAT identifier (optional) pattern: "*.FORMAT" - info: type: file description: Extracted information from the INFO field in the VCF file (optional) pattern: "*.INFO" - genotypes_matrix: type: file description: | Genotypes output as large matrix. Genotypes of each individual on a separate line. Genotypes are represented as 0, 1 and 2, where the number represent that number of non-reference alleles. Missing genotypes are represented by -1 (optional) pattern: "*.012" - genotypes_matrix_individual: type: file description: Details the individuals included in the main genotypes_matrix file (optional) pattern: "*.012.indv" - genotypes_matrix_position: type: file description: Details the site locations included in the main genotypes_matrix file (optional) pattern: "*.012.pos" - impute_hap: type: file description: Phased haplotypes in IMPUTE reference-panel format (optional) pattern: "*.impute.hap" - impute_hap_legend: type: file description: Impute haplotype legend file (optional) pattern: "*.impute.hap.legend" - impute_hap_indv: type: file description: Impute haplotype individuals file (optional) pattern: "*.impute.hap.indv" - ldhat_sites: type: file description: Output data in LDhat format, sites (optional) pattern: "*.ldhat.sites" - ldhat_locs: type: file description: output data in LDhat format, locations (optional) pattern: "*.ldhat.locs" - beagle_gl: type: file description: Genotype likelihoods for biallelic sites (optional) pattern: "*.BEAGLE.GL" - beagle_pl: type: file description: Genotype likelihoods for biallelic sites (optional) pattern: "*.BEAGLE.PL" - ped: type: file description: output the genotype data in PLINK PED format (optional) pattern: "*.ped" - map_: type: file description: output the genotype data in PLINK PED format (optional) pattern: "*.map" - tped: type: file description: output the genotype data in PLINK PED format (optional) pattern: "*.tped" - tfam: type: file description: output the genotype data in PLINK PED format (optional) pattern: "*.tfam" - diff_sites_in_files: type: file description: Sites that are common / unique to each file specified in optional inputs (optional) pattern: "*.diff.sites.in.files" - diff_indv_in_files: type: file description: Individuals that are common / unique to each file specified in optional inputs (optional) pattern: "*.diff.indv.in.files" - diff_sites: type: file description: Discordance on a site by site basis, specified in optional inputs (optional) pattern: "*.diff.sites" - diff_indv: type: file description: Discordance on a individual by individual basis, specified in optional inputs (optional) pattern: "*.diff.indv" - diff_discd_matrix: type: file description: Discordance matrix between files specified in optional inputs (optional) pattern: "*.diff.discordance.matrix" - diff_switch_error: type: file description: Switch errors found between sites (optional) pattern: "*.diff.switch" authors: - "@Mark-S-Hill"