Sambamba

Introduction

Sambamba is a high performance highly parallel robust and fast tool (and library), written in the D programming language, for working with SAM and BAM files.

For more information, please check its website: https://biocontainers.pro/tools/sambamba and its home page on Github.

Versions

• 0.8.2

Commands

• sambamba

Module

You can load the modules by:

module load biocontainers
module load sambamba

Example job

Warning

Using #!/bin/sh -l as shebang in the slurm job script will cause the failure of some biocontainer modules. Please use #!/bin/bash instead.

To run Sambamba on our clusters:

#!/bin/bash
#SBATCH -A myallocation     # Allocation name
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 1
#SBATCH --job-name=sambamba
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out

module --force purge
ml biocontainers sambamba

sambamba view --reference-info input.bam
sambamba view -c -F "mapping_quality >= 40" input.bam