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.