SAM Tools provide various utilities for manipulating alignments in the SAM format, including sorting, merging, indexing and generating alignments in a per-position format.
Documentation
- http://samtools.sourceforge.net
- 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
