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. |
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)