BCFtools

BCFtools is a set of utilities for variant calling and for manipulating variant call format (VCF) and its binary counterpart (BCF) files. It is part of the same project as SAMtools and HTSlib.

BCFtools

License

Free to use and open source under the MIT/Expat License.

Available

Roihu: 1.23.1, via the bio-apps module.

Usage

BCFtools is part of the bio-apps collection on Roihu. Load the bio-apps module tree and then the BCFtools module:

module load bio-apps/v202603
module load bcftools/1.23.1

BCFtools provides many subcommands, for example bcftools view, bcftools call, bcftools mpileup, bcftools stats and bcftools filter. For example, to call variants from an alignment:

bcftools mpileup -f reference.fa aln.bam | bcftools call -mv -Oz -o calls.vcf.gz

Several BCFtools subcommands support the --threads option. For commands using the common BCFtools threading option, additional threads are currently used for compression of compressed BCF (-Ob) or VCF (-Oz) output rather than for parallelizing the main analysis.

Example batch script

#!/bin/bash
#SBATCH --job-name=bcftools
#SBATCH --account=<project>
#SBATCH --output=output_%j.txt
#SBATCH --error=errors_%j.txt
#SBATCH --partition=small
#SBATCH --time=04:00:00
#SBATCH --nodes=1
#SBATCH --ntasks=1
#SBATCH --cpus-per-task=1
#SBATCH --mem-per-cpu=2G

module load bio-apps/v202603
module load bcftools/1.23.1

bcftools mpileup -Ou -f reference.fa aln.bam | bcftools call -mv -Oz -o calls.vcf.gz

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.

Support

CSC Service Desk