sam-tools

Summary

Software Description

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

General Linux

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

module load samtools

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

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/1.9
samtools view -bS sample.sam > out.bam
diff ref_out.bam out.bam