Freebayes

Introduction

Freebayes is a Bayesian genetic variant detector designed to find small polymorphisms, specifically SNPs (single-nucleotide polymorphisms), indels (insertions and deletions), MNPs (multi-nucleotide polymorphisms), and complex events (composite insertion and substitution events) smaller than the length of a short-read sequencing alignment.

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

Versions

  • 1.3.5

  • 1.3.6

Commands

  • freebayes

  • freebayes-parallel

Module

You can load the modules by:

module load biocontainers
module load freebayes

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 Freebayes on our clusters:

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

module --force purge
ml biocontainers freebayes

freebayes -f ref.fa aln.cram >var.vcf