bamtools

Description

C++ API & command-line toolkit for working with BAM data.

Versions

• Anvil: 2.5.2

Module

You can load the modules by:

module load bamtools

Example job

To run bamtools our our clusters:

#!/bin/bash
#SBATCH -A myallocation     # Allocation name
#SBATCH -t 20:00:00
#SBATCH -N 1
#SBATCH -n 24
#SBATCH -p PartitionName
#SBATCH --job-name=bamtools
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out

module load bamtools

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