Description

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

Input

Name
Description
Pattern

0 ()

1 ()

0 ()

0 ()

Output

Name
Description
Pattern

vcf ()

bcf ()

frq ()

frq_count ()

idepth ()

ldepth ()

ldepth_mean ()

gdepth ()

hap_ld ()

geno_ld ()

geno_chisq ()

list_hap_ld ()

list_geno_ld ()

interchrom_hap_ld ()

interchrom_geno_ld ()

tstv ()

tstv_summary ()

tstv_count ()

tstv_qual ()

filter_summary ()

sites_pi ()

windowed_pi ()

weir_fst ()

heterozygosity ()

hwe ()

tajima_d ()

freq_burden ()

lroh ()

relatedness ()

relatedness2 ()

lqual ()

missing_individual ()

missing_site ()

snp_density ()

kept_sites ()

removed_sites ()

singeltons ()

indel_hist ()

hapcount ()

mendel ()

format ()

info ()

genotypes_matrix ()

genotypes_matrix_individual ()

genotypes_matrix_position ()

impute_hap ()

impute_hap_legend ()

impute_hap_indv ()

ldhat_sites ()

ldhat_locs ()

beagle_gl ()

beagle_pl ()

ped ()

map_ ()

tped ()

tfam ()

diff_sites_in_files ()

diff_indv_in_files ()

diff_sites ()

diff_indv ()

diff_discd_matrix ()

diff_switch_error ()

versions ()

Tools

vcftools Documentation

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

License: LGPL
nf-core pipelines with this module
variantcalling
Authors