SAMtools

SAM (Sequence Alignment/Map) format is a generic format for storing large nucleotide sequence alignments. SAM aims to be a format that:


 * Is flexible enough to store all the alignment information generated by various alignment programs;
 * Is simple enough to be easily generated by alignment programs or converted from existing alignment formats;
 * Is compact in file size;
 * Allows most of operations on the alignment to work on a stream without loading the whole alignment into memory;
 * Allows the file to be indexed by genomic position to efficiently retrieve all reads aligning to a locus.

SAM Tools provide various utilities for manipulating alignments in the SAM format, including sorting, merging, indexing and generating alignments in a per-position format.

Project website: http://samtools.sourceforge.net/

Load SGE module
The following Modules files should be loaded for this package: module load samtools/samtools