Sambamba is a high performance modern robust and fast tool (and library), written in the D programming language, for working with SAM and BAM files. Current parallelised functionality is an important subset of samtools functionality, including view, index, sort, markdup, and depth.

References:

• https://academic.oup.com/bioinformatics/article/31/12/2032/214758

• https://github.com/biod/sambamba

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

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

[user@biowulf]$ sinteractive --cpus-per-task=4 --gres=lscratch:10
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 sambamba
[user@cn3144 ~]$ mkdir -p /data/$USER/sambamba && cd /data/$USER/sambamba
[user@cn3144 ~]$ cp $SAMBAMBA_TEST_DATA/* .
[user@cn3144 ~]$ sambamba sort -t $SLURM_CPUS_PER_TASK --tmpdir=lscratch/$SLURM_JOB_ID issue_204.bam
[user@cn3144 ~]$ sambamba view -t $SLURM_CPUS_PER_TASK -c -F "proper_pair" issue_204.bam
[user@cn3144 ~]$ exit
salloc.exe: Relinquishing job allocation 46116226
[user@biowulf ~]$

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

#!/bin/bash
set -e
module load sambamba
sambamba sort -t $SLURM_CPUS_PER_TASK --tmpdir=lscratch/$SLURM_JOB_ID issue_204.bam

Submit this job using the Slurm sbatch command.

sbatch --cpus-per-task=4 --gres=lscratch:10 sambamba.sh

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

cd dir1; sambamba view --reference-info issue_204.bam
cd dir2; sambamba view --header --format=json issue_204.bam
cd dir3; sambamba flagstat -t $SLURM_CPUS_PER_TASK --show-progress issue_204.bam 

Submit this job using the swarm command.

swarm -f sambamba.swarm -t 4 --module sambamba