BamTools

BamTools provides both a programmer's API and an end-user's toolkit for handling BAM files.

BamTools is available as a module on Apocrita.

Usage

To run the default installed version of BamTools, simply load the bamtools module:

$ module load bamtools
$ bamtools --help

usage: bamtools [--help] COMMAND [ARGS]

Available bamtools commands:
    convert
    count
    coverage
    filter
    header
    index
    merge
    random
    resolve
    revert
    sort
    split
    stats

See 'bamtools help COMMAND' for more information on a specific command.

For more information regarding each analysis pipeline, pass the --help switch after the pipeline sub-command (i.e. bamtools convert --help).

Example job

Serial job

Here is an example job running on 1 core and 4GB of memory to convert a bam file to a fastq file:

#!/bin/bash
#$ -cwd
#$ -j y
#$ -pe smp 1
#$ -l h_rt=1:0:0
#$ -l h_vmem=4G

module load bamtools

bamtools convert -format fastq \
                 -in input_alignments.bam \
                 -out output_reads.fastq

Reference

• BamTools GitHub repository
• BamTools project wiki