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SAMtools

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Latest revision as of 10:37, 4 April 2012

This page is a Generic stub.

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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/

[edit] Load SGE module

The following Modules files should be loaded for this package:

module load samtools/samtools