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SAMtools

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

 

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

module load samtools

To see how to get additional help, type

module help samtools

 

The SAMtools programs are availiable through the Galaxy instance on biou.

To make the SAMtools programs availiable through the command line,  csh users should enter the following command:

source /packages/bin/SETUP_BIO_SOFTWARE

To make the SAMtools programs availiable through the command line, bash users should enter the following command:

source /packages/bin/SETUP_BIO_SOFTWARE

 

See more help on SAMTools.