Bazam

Introduction

Bazam is a tool to extract paired reads in FASTQ format from coordinate sorted BAM files. For more information, please check: Docker hub: https://hub.docker.com/r/dockanomics/bazam Home page: https://github.com/ssadedin/bazam

Versions

• 1.0.1

Commands

• bazam

Module

You can load the modules by:

module load biocontainers
module load bazam

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 bazam on our clusters:

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

module --force purge
ml biocontainers bazam