SAMtools

Overview

SAM (Sequence Alignment/Map) format is a generic format for storing large nucleotide sequence alignments. SAM Tools provide various utilities for manipulating alignments in the SAM format, including sorting, merging, indexing and generating alignments in a per-position format.

Version 1.3.1 is available on the CSF (it was compiled with gcc 4.7.0) and includes tabix.
Version 0.1.18 is available on the CSF (it was compiled with gcc 4.4.6)

Restrictions on use

SAMtools is open source, under the MIT License, and available to all users.

Set up procedure

To access SAMtools please load the modulefile:

module load apps/gcc/samtools/1.3.1 

or

module load apps/gcc/samtools/0.1.18 

Running the application

Serial batch job submission

Coming soon …

Parallel batch job submission

Coming soon …

Further info

• The SAMtools website has documentation and an FAQ.
• The old SAMtools website may contain information relevant to releases prior to 0.1.x.