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 --ntasks=1 # (or -n 1) Request 1 core
#SBATCH --mem-per-cpu=1G # Request 1GB RAM per core (1GB total)
#SBATCH --time=1:0:0 # (or -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 --ntasks=1 # (or -n 1) Request 1 core
#SBATCH --mem-per-cpu=1G # Request 1GB RAM per core (1GB total)
#SBATCH --time=1:0:0 # (or -t 1:0:0) Request 1 hour runtime
module load bamutil
bam validate --in example.bam \
--verbose