BamTools

Introduction

BamTools is a programmer API and an end-user toolkit for handling BAM files. This container provides a toolkit-only version (no API to build against).

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

Versions

• 2.5.1

Commands

• bamtools

Module

You can load the modules by:

module load biocontainers
module load bamtools

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 BamTools on our clusters:

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

module --force purge
ml biocontainers bamtools

bamtools convert -format fastq -in in.bam -out out.fastq