For detailed specifications, we refer you to the September 2014 article titled Sequence Alignment/Map Format Specification by the SAM/BAM Format Specification Working Group.

  • For a brief overview, visit the Samtools site on Sourceforge.
  • For information on the related binary version of SAM, see BAM.


The citation for the 2009 Bioinformatics paper introducing the SAM format follows:

Li H.*, Handsaker B.*, Wysoker A., Fennell T., Ruan J., Homer N., Marth G., Abecasis G., Durbin R. and 1000 Genome Project Data Processing Subgroup (2009) The Sequence alignment/map (SAM) format and SAMtools. Bioinformatics, 25, 2078-9. [PMID: 19505943]