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-kitDocker
You can also run VCF-kit with all installed dependencies using docker:
docker run -it andersenlab/vcf-kit vk