SAM 

SAM (Sequence Alignment/Map) format is a generic format for storing large nucleotide sequence alignments. SAM aims to be a format that: 1) Is flexible enough to store all the alignment information generated by various alignment programs; 2) Is simple enough to be easily generated by alignment programs or converted from existing alignment formats; 3) Is compact in file size; 4) Allows most of operations on the alignment to work on a stream without loading the whole alignment into memory; 5) 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. SAMtools is hosted by SourceForge.net. (http://samtools.sourceforge.net/ )