Skip to content

AndersenLab/VCF-kit

master
Switch branches/tags

Name already in use

A tag already exists with the provided branch name. Many Git commands accept both tag and branch names, so creating this branch may cause unexpected behavior. Are you sure you want to create this branch?
Code

Build Status Coverage Status Documentation Status

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.

Installation

VCF-Kit has been upgraded to Python 3

VCF-kit has been tested with Python 3.6. VCF-kit makes use of additional software for a variety of tasks:

  • bwa (v 0.7.12)
  • samtools (v 1.3)
  • bcftools (v 1.3)
  • blast (v 2.2.31+)
  • muscle (v 3.8.31)
  • primer3 (v 2.5.0)

You can install these dependencies and VCF-kit using conda, or you can use a Docker image.

Conda

conda config --add channels bioconda
conda config --add channels conda-forge
conda create -n vcf-kit \
  danielecook::vcf-kit=0.2.6 \
  "bwa>=0.7.17" \
  "samtools>=1.10" \
  "bcftools>=1.10" \
  "blast>=2.2.31" \
  "muscle>=3.8.31" \
  "primer3>=2.5.0"

conda activate vcf-kit

Docker

You can also run VCF-kit with all installed dependencies using docker:

docker run -it andersenlab/vcf-kit vk