Bcftools

Introduction

Bcftools is a program for variant calling and manipulating files in the Variant Call Format (VCF) and its binary counterpart BCF.

For more information, please check:
BioContainers: https://biocontainers.pro/tools/bcftools
Home page: https://samtools.github.io/bcftools/bcftools.html

Versions

  • 1.13

  • 1.14

  • 1.17

Commands

  • bcftools

  • color-chrs.pl

  • guess-ploidy.py

  • plot-roh.py

  • plot-vcfstats

  • run-roh.pl

  • vcfutils.pl

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 bcftools on our clusters:

#!/bin/bash
#SBATCH -p PartitionName  # batch, gpu, preempt, mpi or your group's own partition
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 1
#SBATCH -c 4
#SBATCH --mem=8G
#SBATCH --job-name=bcftools
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out

module purge
module load bcftools/XXXX ### you can run *module avail bcftools* to check all available versions

bcftools query -f '%CHROM %POS %REF %ALT\n' file.bcf
bcftools polysomy -v -o outdir/ file.vcf

# Variant calling
bcftools mpileup -f reference.fa alignments.bam | bcftools call -mv -Ob -o calls.bcf