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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 latest 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 memory:

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

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
#$ -cwd
#$ -j y
#$ -pe smp 1
#$ -l h_rt=1:0:0
#$ -l h_vmem=1G

module load bamutil

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

References