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