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VCF-kit - Documentation

VCF-kit is a command-line based collection of utilities for performing analysis on Variant Call Format (VCF) files. A summary of the commands is provided below.

Command Description
calc Obtain frequency/count of genotypes and alleles.
call Compare variants identified from sequences obtained through alternative methods against a VCF.
filter Filter variants with a minimum or maximum number of REF, HET, ALT, or missing calls.
geno Various operations at the genotype level.
genome Reference genome processing and management.
hmm Hidden-markov model for use in imputing genotypes from parental genotypes in linkage studies.
phylo Generate dendrograms from a VCF.
primer Generate primers for variant validation.
rename Add a prefix, suffix, or substitute a string in sample names.
tajima Calculate Tajima’s D.
vcf2tsv Convert a VCF to TSV.



conda config --add channels bioconda
conda create -n vcf-kit python=2.7 vcfkit


You may need to install matplotlib. On linux this can be done with:

sudo apt-get build-dep python-matplotlib

On OSX it can be installed using:

pip install matplotlib  

You may need to install a few additional dependencies:

pip install yahmm
pip install numpy
pip install VCF-kit

Installing Dependencies:

In addition to python, VCF-kit requires that a number of additional programs be installed. We recommend using homebrew to manage dependencies. vk setup can be used to install these dependencies. Alternatively, you may use:

brew install bwa samtools bcftools blast muscle

vk setup requires homebrew (or if on linux, linux-brew) to install programs used by VCF-kit. The programs are listed below followed by the versions they have been tested with.

  • bwa (v 0.7.12)
  • samtools (v 1.3)
  • bcftools (v 1.3)
  • blast (v 2.2.31+)
  • muscle (v 3.8.31)
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