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]

See also: HTSlib, VCF2MAF

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

See more help on SAMTools.