VCFtools
VCFtools is a program package designed for working with VCF files, such as those
generated by the 1000 Genomes Project. It provides tools for filtering, comparing and
computing statistics on variant call data, as well as a set of Perl modules and scripts
(vcf-*).
License
Free to use and open source under GNU LGPLv3.
Available
- Roihu: 0.1.17, via the
bio-appsmodule.
Usage
VCFtools is part of the bio-apps collection on Roihu. Load the bio-apps module tree and then the VCFtools module:
The main program is vcftools. For example, to keep only biallelic SNPs and write a
new VCF:
vcftools --gzvcf input.vcf.gz --remove-indels --min-alleles 2 --max-alleles 2 --recode --out filtered
The accompanying Perl scripts (such as vcf-sort and vcf-concat) are also available;
the module sets PERL5LIB so they find the bundled Vcf.pm module.
Example batch script
#!/bin/bash
#SBATCH --job-name=vcftools
#SBATCH --account=<project>
#SBATCH --output=output_%j.txt
#SBATCH --error=errors_%j.txt
#SBATCH --partition=small
#SBATCH --time=02:00:00
#SBATCH --nodes=1
#SBATCH --ntasks=1
#SBATCH --cpus-per-task=1
#SBATCH --mem=4G
module load bio-apps/v202603
module load vcftools/0.1.17
vcftools --gzvcf input.vcf.gz --remove-indels --min-alleles 2 --max-alleles 2 --recode --out filtered
Replace <project> with your CSC project (for example project_2001234).
See creating a batch job script for Roihu for more information about running batch jobs.