Quick Links Documentation Notes Interactive job Batch job Swarm of jobs

BamTools provides both a programmer's API and an end-user's toolkit for handling BAM files. It was developed by Derek Barnett in the Marth lab at Boston College.

References:

• https://academic.oup.com/bioinformatics/article/27/12/1691/255399

• https://github.com/pezmaster31/bamtools/wiki

• Module Name: bamtools (see the modules page for more information)

Allocate an interactive session and run the program. Sample session:

[user@biowulf]$ sinteractive
salloc.exe: Pending job allocation 46116226
salloc.exe: job 46116226 queued and waiting for resources
salloc.exe: job 46116226 has been allocated resources
salloc.exe: Granted job allocation 46116226
salloc.exe: Waiting for resource configuration
salloc.exe: Nodes cn3144 are ready for job

[user@cn3144 ~]$ module load bamtools
[user@cn3144 ~]$ bamtools convert -format fastq -in in.bam -out out.fastq
[user@cn3144 ~]$ exit
salloc.exe: Relinquishing job allocation 46116226
[user@biowulf ~]$

Create a batch input file (e.g. bamtools.sh). For example:

#!/bin/bash
set -e
module load bamtools
bamtools convert -format fastq -in in.bam -out out.fastq

Submit this job using the Slurm sbatch command.

sbatch [--mem=#] bamtools.sh

Create a swarmfile (e.g. bamtools.swarm). For example:

cd dir1; bamtools convert -format fastq -in in.bam -out out.fastq
cd dir2; bamtools convert -format fastq -in in.bam -out out.fastq
cd dir3; bamtools convert -format fastq -in in.bam -out out.fastq

Submit this job using the swarm command.

swarm -f bamtools.swarm [-g #] --module bamtools

where

-g #	Number of Gigabytes of memory required for each process (1 line in the swarm command file)
--module bamtools	Loads the bamtools module for each subjob in the swarm