Julia utilities for handling VCF files

VCFTools.jl implements some Julia utilities for handling VCF files. This package heavily uses the VCF parser developed in the BioJulia/GeneticVariation.jl package, which has been superseded by VariantCallFormal.jl

Package Features

  • Calculate genotype statistics (minor allele frequencies, minor allele, count of missing genotypes, etc) from a VCF file.
  • Extract specific data fields from a VCF file.
  • Filtering/subsetting VCF files.
  • Match markers in two VCF files according to ID.
  • Calculation of Genetic Relationship Matrix.
  • Rank SNPs by their ancestry informativeness.
  • Saving numeric matrix into VCF file


Within Julia,

using Pkg
pkg"add VCFTools"

This package supports Julia v1.5+.

Manual Outline