Samtools

Introduction

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

For more information, please check:

Docker hub: https://hub.docker.com/r/staphb/samtools

Home page: https://github.com/samtools/samtools

Versions

• 1.16

• 1.17

Commands

• ace2sam

• blast2sam.pl

• bowtie2sam.pl

• export2sam.pl

• fasta-sanitize.pl

• interpolate_sam.pl

• maq2sam-long

• maq2sam-short

• md5fa

• md5sum-lite

• novo2sam.pl

• plot-ampliconstats

• plot-bamstats

• psl2sam.pl

• sam2vcf.pl

• samtools

• samtools.pl

• seq_cache_populate.pl

• soap2sam.pl

• wgsim

• wgsim_eval.pl

• zoom2sam.pl

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 -p PartitionName  # batch, gpu, preempt, mpi or your group's own partition
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 1
#SBATCH -c 4
#SBATCH --mem=8G
#SBATCH --job-name=samtools
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out

module purge
module load samtools/XXXX ### you can run *module avail samtools* to check all available versions