The SAM (Sequence Alignment/Map) format is a generic format for storing large nucleotide sequnce alignments. SAMtools provides various utilities for manipulating alignments in the SAM format, including sorting, merging, indexing and generating alignments in a per-position format.

The SAMtools home page is at

Available modules

Packages with modules

Module NeSI Cluster
SAMtools/1.3.1-gimkl-2017a pan
SAMtools/0.1.19-foss-2015a pan
SAMtools/0.1.19-goolf-1.5.14 pan
SAMtools/0.1.19-intel-2015a pan
SAMtools/1.2-goolf-1.5.14 pan
SAMtools/1.3-foss-2015a pan

Licensing requirements

SAMtools is released at no cost under the terms of the MIT/Expat licence. To obtain a copy of the current SAMtools licence, please see [].

Example scripts

Example script for the Pan cluster

#!/bin/bash -e

#SBATCH --job-name      SAMtools_job
#SBATCH --account       nesi99999
#SBATCH --time          01:00:00
#SBATCH --mem-per-cpu   4G
#SBATCH --output        SAMtools_job.%j.out # Include the job ID in the names
#SBATCH --error         SAMtools_job.%j.err # of the output and error files

module load SAMtools/1.2-goolf-1.5.14

samtools view SAMtools_job.sam


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