Software: Freebayes
Description
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.
Available Versions
| Unspecified: | 1.3.5 1.3.6 |
|---|
For more information, please check its website: https://biocontainers.pro/tools/freebayes and its home page on Github.
Commands
- freebayes
- freebayes-parallel
Module
You can load the modules by:
module load biocontainers
module load freebayes
Example job
Using
#!/bin/sh -las shebang in the slurm job script will cause the failure of some biocontainer modules. Please use#!/bin/bashinstead.
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