SAMtools

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  
* 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.

Access

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

Usage on Owens

Set-up

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

Set-up

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

Further Reading

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