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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
#SBATCH -n 1               # (or --ntasks=1) Request 1 core
#SBATCH --mem-per-cpu=4G   # Request 4GB RAM per core
#SBATCH -t 1:0:0           # Request 1 hour runtime

module load bamtools

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

Reference