bamtools

Software Summary

Mesabi

Default Module:

2.5.2-gcc-8.2.0-vzfrpdp

Other Modules Available:

2.5.2-gcc-13.1.0-6ce7c3p, 2.5.2-gcc-8.2.0-vzfrpdp, 2.5.1, 20120608

Last Updated On:

Tuesday, November 14, 2023

Mesabi K40

Default Module:

Other Modules Available:

Last Updated On:

Mangi

Default Module:

2.5.2-gcc-8.2.0-vzfrpdp

Other Modules Available:

2.5.2-gcc-13.1.0-6ce7c3p, 2.5.2-gcc-8.2.0-vzfrpdp, 2.5.1, 20120608

Last Updated On:

Tuesday, November 14, 2023

Mangi v100

Default Module:

Other Modules Available:

Last Updated On:

NICE

Default Module:

Other Versions Available:

Last Updated On:

Tuesday, November 14, 2023

Support Level:

Primary Support

Software Access Level:

Open Access

Home Page:

Link

Software Categories:

Genetics

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).

Software Documentation

Software Documentation Tabs

General Linux

To run this software interactively in a Linux environment run the commands:

module load bamtools
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 small,large,ram256g,ram1t
module load bamtools/20120608
bamtools stats -in out.bam