The Sequence Alignment/Map format and SAMtools.
CONCLUSIONS
The Sequence Alignment/Map (SAM) format is a generic alignment format for storing read alignments against reference sequences, supporting short and long reads (up to 128 Mbp) produced by different sequencing platforms. It is flexible in style, compact in size, efficient in random access and is the format in which alignments from the 1000 Genomes Project are released. SAMtools implements various utilities for post-processing alignments in the SAM format, such as indexing, variant caller and alignment viewer, and thus provides universal tools for processing read alignments.


BACKGROUND
http://samtools.sourceforge.net.
Li
Heng
H
Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, CB10 1SA, UK, Broad Institute of MIT and Harvard, Cambridge, MA 02141, USA.
Handsaker
Bob
B
Wysoker
Alec
A
Fennell
Tim
T
Ruan
Jue
J
Homer
Nils
N
Marth
Gabor
G
Abecasis
Goncalo
G
Durbin
Richard
R
D000465:Algorithms; D001483:Base Sequence; D019295:Computational Biology / Q000379:methods*; D016678:Genome; D023281:Genomics; D008969:Molecular Sequence Data; D016415:Sequence Alignment / Q000379:methods*; D017422:Sequence Analysis, DNA / Q000379:methods*; D012984:Software