SAMTools
SAMTools 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-2
To see what versions of SAMTools are available and if there is more than one, which is the default, along with some help, type
module spider samtools
To use SAMTools, include a command like this in your batch script or interactive session to load the SAMTools module: (note ‘module load’ is case-sensitive):
module load samtools
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
