# samtools

## Summary

+ **Module Name:** samtools
+ **Support Level:** Primary Support
+ **Software Access Level:** Open Access
+ **Home Page:** [http://sourceforge.net/projects/samtools/](http://sourceforge.net/projects/samtools/)

## Software Description

SAM (Sequence Alignment/Map) is a flexible generic format for storing
nucleotide sequence alignment. SAMtools provide efficient utilities for
manipulating alignments in the SAM and Bam formats.
## General Linux

Depending on where you are working, there may be more than one version of SAMtools available.
To see which modules are available for loading you can run:

	`module avail samtools`
	
To load this module for use in a Linux environment, you can run the command:

	`module load samtools/<version>`

To load version 1.21 use:

	`module load samtools/1.21`

## Slurm Example

```
	#!/bin/bash
	#SBATCH --job-name="rfm_RunSamtoolsTest_job"
	#SBATCH --ntasks=1
	#SBATCH --ntasks-per-node=1
	#SBATCH --output=rfm_RunSamtoolsTest_job.out
	#SBATCH --error=rfm_RunSamtoolsTest_job.err
	#SBATCH --time=0:10:0
	#SBATCH -p msismall
	module load samtools/1.21
	samtools view -bS sample.sam > out.bam
	diff ref_out.bam out.bam
```