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BCFtools

BCFtools are a set of utilities that manipulate variant calls in the Variant Call Format (VCF) and its binary counterpart, BCF.

BCFtools is available as a module on Apocrita.

Usage

To run the default installed version of BCFtools, simply load the bcftoolsmodule:

$ module load bcftools
$ bcftools

Program: bcftools (Tools for variant calling and manipulating VCFs and BCFs)
Version: <VERSION> (using htslib <VERSION>)

Usage:   bcftools [--version|--version-only] [--help] <command> <argument>

Example jobs

Serial jobs

Here is an example job running on 1 core and 2GB of memory to create an index for the compressed .bcf file named genome_variants.bcf:

  • The -c option will generate the index in CSI format.
  • The -f will rewrite any existing .csi files.
#!/bin/bash
#SBATCH -n 1               # (or --ntasks=1) Request 1 core
#SBATCH --mem-per-cpu=2G   # Request 2GB RAM per core
#SBATCH -t 1:0:0           # Request 1 hour runtime

module load bcftools

bcftools index -c -f genome_variants.bcf

Here is an example job running on 1 core and 2GB of memory to extract stats from the output.chk file to plot graphs and generate a PDF.

#!/bin/bash
#SBATCH -n 1               # (or --ntasks=1) Request 1 core
#SBATCH --mem-per-cpu=2G   # Request 2GB RAM per core
#SBATCH -t 1:0:0           # Request 1 hour runtime

module load bcftools

plot-vcfstats output.chk

Reference