On September 22nd, OSC switched to Slurm for job scheduling and resource management on the Pitzer Cluster, along with the deployment of the new Pitzer hardware. We are in the process of updating the example job scripts for each software. If a Slurm example is not yet available, please consult our general Slurm information page or contact OSC help.


SAM format is a generic format for storing large nucleotide sequence alignments. SAMtools provide various utilities for manipulating alignments in the SAM format, including sorting, merging, indexing and generating alignments in a per-position format.

Availability and Restrictions

The following versions of SAMtools are available on OSC clusters:

Version Owens Pitzer
1.3.1 X  
1.6 X  
1.8   X
1.9 X  
1.10 X* X*
* Current default version

You can use  module spider samtools to view available modules for a given machine. Feel free to contact OSC Help if you need other versions for your work.


SAMtools is available to all OSC users. If you have any questions, please contact OSC Help.

Publisher/Vendor/Repository and License Type

Genome Research Ltd., Open source


Usage on Owens


To configure your environment for use of SAMtools, run the following command:    module load samtools  . The default version will be loaded. To select a particular SAMtools version, use    module load samtools/version  . For example, use   module load samtools/1.3.1   to load SAMtools 1.3.1.

Usage on Pitzer


To configure your environment for use of SAMtools, run the following command:    module load samtools  . The default version will be loaded. 

Further Reading

Fields of Science: