sam-tools

Genetics

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.


Info

Module Name

samtools

Last Updated On

11/14/2023

Support Level

Primary Support

Software Access Level

Open Access

Home Page

http://sourceforge.net/projects/samtools/

Documentation

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.

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 small,large,ram256g,ram1t
module load samtools/1.9
samtools view -bS sample.sam > out.bam
diff ref_out.bam out.bam

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

Agate Modules

Default

1.9

Other Modules

1.3_gcc-4.9.2_haswell, 1.5_gcc-7.2.0_haswell, 1.7_gcc-7.2.0_haswell, 1.9, 1.16.1-gcc-8.2.0-egljrr3, 1.10, 1.14, 1.17, 1.9, 1.5, 1.6, 1.7, 1.9

Mangi Modules

Default

1.16.1-gcc-8.2.0-egljrr3

Other Modules

1.16.1-gcc-8.2.0-egljrr3, 1.10, 1.14, 1.17, 1.9, 1.5, 1.6, 1.7, 1.9

Mesabi Modules

Default

1.9

Other Modules

1.3_gcc-4.9.2_haswell, 1.5_gcc-7.2.0_haswell, 1.7_gcc-7.2.0_haswell, 1.9, 1.16.1-gcc-8.2.0-egljrr3, 1.10, 1.14, 1.17, 1.9, 1.5, 1.6, 1.7, 1.9