VCFtools

Introduction

VCFtools is a program package designed for working with VCF files, such as those generated by the 1000 Genomes Project. The aim of VCFtools is to provide easily accessible methods for working with complex genetic variation data in the form of VCF files.

For more information, please check its website: https://biocontainers.pro/tools/vcftools and its home page on Github.

Versions

• 0.1.16

Commands

• vcftools

Module

You can load the modules by:

module load biocontainers
module load vartrix

Example job

Warning

Using #!/bin/sh -l as shebang in the slurm job script will cause the failure of some biocontainer modules. Please use #!/bin/bash instead.

To run VCFtools on our clusters:

#!/bin/bash
#SBATCH -A myallocation     # Allocation name
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 1
#SBATCH --job-name=vcftools
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out

module --force purge
ml biocontainers vcftools

vcftools --vcf input_data.vcf --chr 1 \
    --from-bp 1000000 --to-bp 2000000