Genotype Imputation and Population Genomics Efficiently from Variant Call Formatted (VCF) Files
Calculate Allele Frequencies from Genotype Matrix
Dxy
FixedSites
Fst
GenoPop-Impute
Heterozygosity Rate
OneDimSFS
Pi
PrivateAlleles
SegregatingSites
Separate Genotype Matrix by Populations
SingletonSites
TajimasD
TwoDimSFS
WattersonsTheta
Tools for efficient processing of large, whole genome genotype data sets in variant call format (VCF). It includes several functions to calculate commonly used population genomic metrics and a method for reference panel free genotype imputation, which is described in the preprint Gurke & Mayer (2024) <doi:10.22541/au.172515591.10119928/v1>.