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BamUtil

BamUtil is a collection of programs that perform operations on SAM and BAM files.

BamUtil is available as a module on Apocrita.

Usage

To run the default installed version of BamUtil, simply load the bamutil module:

module load bamutil

For usage documentation, run bam -h.

Example jobs

Serial jobs

Here is an example job to clip overlapping read pairs, running on 1 core and 1GB of memory:

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

module load bamutil

bam clipOverlap --in example.bam \
                --out clipped.bam

Here is an example job to validate and check a BAM file format (also works for SAM files) and printing verbose statistics, running on 1 core and 1GB memory:

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

module load bamutil

bam validate --in example.bam \
             --verbose

References