modules/vcftools

A set of tools written in Perl and C++ for working with VCF files

VCFtoolsVCFsort

https://github.com/nf-core/modules/[...]/modules/nf-core/vcftools

Description

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

]

`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

`meta` (map)

Groovy Map containing sample information
e.g. [ id:‘test’, single_end

]

`versions` (file)

File containing software versions

versions.yml

`vcf` (file)

vcf file (optional)

*.vcf

`bcf` (file)

bcf file (optional)

*.bcf

`frq` (file)

Allele frequency for each site (optional)

*.frq

`frq_count` (file)

Allele counts for each site (optional)

*.frq.count

`idepth` (file)

mean depth per individual (optional)

*.idepth

`ldepth` (file)

depth per site summed across individuals (optional)

*.ildepth

`ldepth_mean` (file)

mean depth per site calculated across individuals (optional)

*.ldepth.mean

`gdepth` (file)

depth for each genotype in vcf file (optional)

*.gdepth

`hap_ld` (file)

r2, D, and D’ statistics using phased haplotypes (optional)

*.hap.ld

`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` (file)

test for genotype independence via the chi-squared statistic (optional)

*.geno.chisq

`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` (file)

r2 statistics of the sites contained in the provided input file verses all other sites (optional)

*.list.geno.ld

`interchrom_hap_ld` (file)

r2 statistics for sites (haplotypes) on different chromosomes (optional)

*.interchrom.hap.ld

`interchrom_geno_ld` (file)

r2 statistics for sites (genotypes) on different chromosomes (optional)

*.interchrom.geno.ld

`tstv` (file)

Transition / Transversion ratio in bins of size defined in options (optional)

*.TsTv

`tstv_summary` (file)

Summary of all Transitions and Transversions (optional)

*.TsTv.summary

`tstv_count` (file)

Transition / Transversion ratio as a function of alternative allele count (optional)

*.TsTv.count

`tstv_qual` (file)

Transition / Transversion ratio as a function of SNP quality threshold (optional)

*.TsTv.qual

`filter_summary` (file)

Summary of the number of SNPs and Ts/Tv ratio for each FILTER category (optional)

*.FILTER.summary

`sites_pi` (file)

Nucleotide divergency on a per-site basis (optional)

*.sites.pi

`windowed_pi` (file)

Nucleotide diversity in windows, with window size determined by options (optional)

*windowed.pi

`weir_fst` (file)

Fst estimate from Weir and Cockerham’s 1984 paper (optional)

*.weir.fst

`heterozygosity` (file)

Heterozygosity on a per-individual basis (optional)

*.het

`hwe` (file)

Contains the Observed numbers of Homozygotes and Heterozygotes and the corresponding Expected numbers under HWE (optional)

*.hwe

`tajima_d` (file)

Tajima’s D statistic in bins with size of the specified number in options (optional)

*.Tajima.D

`freq_burden` (file)

Number of variants within each individual of a specific frequency in options (optional)

*.ifreqburden

`lroh` (file)

Long Runs of Homozygosity (optional)

*.LROH

`relatedness` (file)

Relatedness statistic based on the method of Yang et al, Nature Genetics 2010 (doi:10.1038/ng.608) (optional)

*.relatedness

`relatedness2` (file)

Relatedness statistic based on the method of Manichaikul et al., BIOINFORMATICS 2010 (doi:10.1093/bioinformatics/btq559) (optional)

*.relatedness2

`lqual` (file)

per-site SNP quality (optional)

*.lqual

`missing_individual` (file)

Missingness on a per-individual basis (optional)

*.imiss

`missing_site` (file)

Missingness on a per-site basis (optional)

*.lmiss

`snp_density` (file)

Number and density of SNPs in bins of size defined by option (optional)

*.snpden

`kept_sites` (file)

All sites that have been kept after filtering (optional)

*.kept.sites

`removed_sites` (file)

All sites that have been removed after filtering (optional)

*.removed.sites

`singeltons` (file)

Location of singletons, and the individual they occur in (optional)

*.singeltons

`indel_hist` (file)

Histogram file of the length of all indels (including SNPs) (optional)

*.indel_hist

`hapcount` (file)

Unique haplotypes within user specified bins (optional)

*.hapcount

`mendel` (file)

Mendel errors identified in trios (optional)

*.mendel

`format` (file)

Extracted information from the genotype fields in the VCF file relating to a specfied FORMAT identifier (optional)

*.FORMAT

`info` (file)

Extracted information from the INFO field in the VCF file (optional)

*.INFO

`genotypes_matrix` (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` (file)

Details the individuals included in the main genotypes_matrix file (optional)

*.012.indv

`genotypes_matrix_position` (file)

Details the site locations included in the main genotypes_matrix file (optional)

*.012.pos

`impute_hap` (file)

Phased haplotypes in IMPUTE reference-panel format (optional)

*.impute.hap

`impute_hap_legend` (file)

Impute haplotype legend file (optional)

*.impute.hap.legend

`impute_hap_indv` (file)

Impute haplotype individuals file (optional)

*.impute.hap.indv

`ldhat_sites` (file)

Output data in LDhat format, sites (optional)

*.ldhat.sites

`ldhat_locs` (file)

output data in LDhat format, locations (optional)

*.ldhat.locs

`beagle_gl` (file)

Genotype likelihoods for biallelic sites (optional)

*.BEAGLE.GL

`beagle_pl` (file)

Genotype likelihoods for biallelic sites (optional)

*.BEAGLE.PL

`ped` (file)

output the genotype data in PLINK PED format (optional)

*.ped

`map_` (file)

output the genotype data in PLINK PED format (optional)

*.map

`tped` (file)

output the genotype data in PLINK PED format (optional)

*.tped

`tfam` (file)

output the genotype data in PLINK PED format (optional)

*.tfam

`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` (file)

Individuals that are common / unique to each file specified in optional inputs (optional)

*.diff.indv.in.files

`diff_sites` (file)

Discordance on a site by site basis, specified in optional inputs (optional)

*.diff.sites

`diff_indv` (file)

Discordance on a individual by individual basis, specified in optional inputs (optional)

*.diff.indv

`diff_discd_matrix` (file)

Discordance matrix between files specified in optional inputs (optional)

*.diff.discordance.matrix

`diff_switch_error` (file)

Switch errors found between sites (optional)

*.diff.switch

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

http://vcftools.sourceforge.net http://vcftools.sourceforge.net/man_latest

modules/vcftools

Description

Input

meta (map)

variant_file (file)

bed (file)

diff_variant_file (file)

Output

meta (map)

versions (file)

vcf (file)

bcf (file)

frq (file)

frq_count (file)

idepth (file)

ldepth (file)

ldepth_mean (file)

gdepth (file)

hap_ld (file)

geno_ld (file)

geno_chisq (file)

list_hap_ld (file)

list_geno_ld (file)

interchrom_hap_ld (file)

interchrom_geno_ld (file)

tstv (file)

tstv_summary (file)

tstv_count (file)

tstv_qual (file)

filter_summary (file)

sites_pi (file)

windowed_pi (file)

weir_fst (file)

heterozygosity (file)

hwe (file)

tajima_d (file)

freq_burden (file)

lroh (file)

relatedness (file)

relatedness2 (file)

lqual (file)

missing_individual (file)

missing_site (file)

snp_density (file)

kept_sites (file)

removed_sites (file)

singeltons (file)

indel_hist (file)

hapcount (file)

mendel (file)

format (file)

info (file)

genotypes_matrix (file)

genotypes_matrix_individual (file)

genotypes_matrix_position (file)

impute_hap (file)

impute_hap_legend (file)

impute_hap_indv (file)

ldhat_sites (file)

ldhat_locs (file)

beagle_gl (file)

beagle_pl (file)

ped (file)

map_ (file)

tped (file)

tfam (file)

diff_sites_in_files (file)

diff_indv_in_files (file)

diff_sites (file)

diff_indv (file)

diff_discd_matrix (file)

diff_switch_error (file)

included in

maintainer

get in touch

Tools

vcftools LGPL

`meta` (map)

`variant_file` (file)

`bed` (file)

`diff_variant_file` (file)

`meta` (map)

`versions` (file)

`vcf` (file)

`bcf` (file)

`frq` (file)

`frq_count` (file)

`idepth` (file)

`ldepth` (file)

`ldepth_mean` (file)

`gdepth` (file)

`hap_ld` (file)

`geno_ld` (file)

`geno_chisq` (file)

`list_hap_ld` (file)

`list_geno_ld` (file)

`interchrom_hap_ld` (file)

`interchrom_geno_ld` (file)

`tstv` (file)

`tstv_summary` (file)

`tstv_count` (file)

`tstv_qual` (file)

`filter_summary` (file)

`sites_pi` (file)

`windowed_pi` (file)

`weir_fst` (file)

`heterozygosity` (file)

`hwe` (file)

`tajima_d` (file)

`freq_burden` (file)

`lroh` (file)

`relatedness` (file)

`relatedness2` (file)

`lqual` (file)

`missing_individual` (file)

`missing_site` (file)

`snp_density` (file)

`kept_sites` (file)

`removed_sites` (file)

`singeltons` (file)

`indel_hist` (file)

`hapcount` (file)

`mendel` (file)

`format` (file)

`info` (file)

`genotypes_matrix` (file)

`genotypes_matrix_individual` (file)

`genotypes_matrix_position` (file)

`impute_hap` (file)

`impute_hap_legend` (file)

`impute_hap_indv` (file)

`ldhat_sites` (file)

`ldhat_locs` (file)

`beagle_gl` (file)

`beagle_pl` (file)

`ped` (file)

`map_` (file)

`tped` (file)

`tfam` (file)

`diff_sites_in_files` (file)

`diff_indv_in_files` (file)

`diff_sites` (file)

`diff_indv` (file)

`diff_discd_matrix` (file)

`diff_switch_error` (file)

vcftools
LGPL