SAM Tools provide various utilities for manipulating alignments in the SAM format, including sorting, merging, indexing and generating alignments in a per-position format.


  • 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 , The Sequence alignment/map (SAM) format and SAMtools. Bioinformatics, 25, 2078-9. (2009) [PMID: 19505943]

Usage on Bridges

Use a command like this in your batch script or interactive session to load the SAMtools module

module load samtools

See all the SAMtools versions available by typing

module available samtools

To see how to get additional help, type

module help samtools

See more help on SAMTools.