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samtools

Summary

• Module Name: samtools

• Support Level: Primary Support

• Software Access Level: Open Access

• Home Page: 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