bamtools

Summary

• Module Name: bamtools

• Support Level: Primary Support

• Software Access Level: Open Access

• Home Page: https://github.com/pezmaster31/bamtools

Software Description

BamTools provides both a programmer’s API and an end-user’s toolkit for handling BAM files (SAMtools is a superior SAM/BAM toolkit).

General Linux

To load this module for use in a Linux environment, you can run the command:

module load bamtools

Depending on where you are working, there may be more than one version of bamtools available. To see which modules are available for loading you can run:

module avail bamtools

Slurm Example

#!/bin/bash
#SBATCH --job-name="rfm_RunBamtoolsTest_job"
#SBATCH --ntasks=1
#SBATCH --ntasks-per-node=1
#SBATCH --output=rfm_RunBamtoolsTest_job.out
#SBATCH --error=rfm_RunBamtoolsTest_job.err
#SBATCH --time=0:10:0
#SBATCH -p msismall
module load bamtools/20120608
bamtools stats -in out.bam