Biobambam2 is a toolkit that contains tools for early stage alignment file processing. The following tools are provided:

• bamsormadup: parallel sorting and duplicate marking
• bamcollate2: reads BAM and writes BAM reordered such that alignment or collated by query name
• bammarkduplicates: reads BAM and writes BAM with duplicate alignments marked using the BAM flags field
• bammaskflags: reads BAM and writes BAM while masking (removing) bits from the flags column
• bamrecompress: reads BAM and writes BAM with a defined compression setting. This tool is capable of multi-threading.
• bamsort: reads BAM and writes BAM resorted by coordinates or query name
• bamtofastq: reads BAM and writes FastQ; output can be collated or uncollated by query name

• biobambam2 Main Site

• Module Name: biobambam2 (see the modules page for more information)

Allocate an interactive session and run the program.
Sample session with bamsort example (user input in bold):

[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 biobambam2

[user@cn3144 ~]$ bamsort SO=queryname <wgEncodeUwRepliSeqBg02esG1bAlnRep1.bam >out.bam
[V] Reading alignments from source.
[V] 1M
[V] read 1784867 alignments
[V] producing sorted output
[V]1
[V] wrote 1784867 alignments

[user@cn3144 ~]$ exit
salloc.exe: Relinquishing job allocation 46116226
[user@biowulf ~]$

Create a batch input file (e.g. biobambam2.sh). For example:

#!/bin/bash
set -e
module load biobambam2
cd /data/username
bamsort SO=queryname <wgEncodeUwRepliSeqBg02esG1bAlnRep1.bam >out.bam

Submit this job using the Slurm sbatch command.

sbatch [--cpus-per-task=#] [--mem=#] biobambam2.sh

Create a swarmfile (e.g. biobambam2.swarm). For example:

bamsort SO=queryname <input1.bam >output1.bam
bamsort SO=queryname <input2.bam >output2.bam
bamsort SO=queryname <input3.bam >output3.bam
bamsort SO=queryname <input4.bam >output4.bam

Submit this job using the swarm command.

swarm -f biobambam2.swarm [-g #] [-t #] --module biobambam2