Purdue University

Commands

• bcftools
• color-chrs.pl
• guess-ploidy.py
• plot-roh.py
• plot-vcfstats
• run-roh.pl
• vcfutils.pl

Module

You can load the modules by:

module load biocontainers
module load bcftools

Example job

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

module --force purge
ml biocontainers bcftools

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