Samtools

Introduction

Samtools is a set of utilities for the Sequence Alignment/Map (SAM) format.

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

Versions

  • 1.15

  • 1.16

  • 1.17

  • 1.9

Commands

  • samtools

  • ace2sam

  • htsfile

  • maq2sam-long

  • maq2sam-short

  • tabix

  • wgsim

Module

You can load the modules by:

module load biocontainers
module load samtools

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 Samtools on our clusters:

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

module --force purge
ml biocontainers samtools