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 | Cardinal |
|---|---|---|---|
| 1.3.1 | X | ||
| 1.6 | X | ||
| 1.8 | X | ||
| 1.9 | X | ||
| 1.10 | X* | X* | |
| 1.16.1 | X | X | |
| 1.17 | 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
Service:
Fields of Science:
