Bedops
Bedops is an open-source command-line toolkit that performs highly efficient and scalable Boolean and other set operations, statistical calculations, archiving, conversion and other management of genomic data of arbitrary scale. Tasks can be easily split by chromosome for distributing whole-genome analyses across a computational cluster.
Documentation
- http://bedops.readthedocs.org
- http://code.google.com/p/bedops/
- Shane Neph, M. Scott Kuehn, Alex P. Reynolds, Eric Haugen, Robert E. Thurman, Audra K. Johnson, Eric Rynes, Matthew T. Maurano, Jeff Vierstra, Sean Thomas, Richard Sandstrom, Richard Humbert,and John A. Stamatoyannopoulos, BEDOPS: high performance genomic feature operations. Bioinformatics 28 (14): 1919-1920 (2012). doi:10.1093/bioinformatics/bts277
Usage on Bridges-2
To see what versions of Bedops are available and if there is more than one, which is the default, along with some help, type
module spider bedops
To use Bedops, include a command like this in your batch script or interactive session to load the BEDOPS module: (note ‘module load’ is case-sensitive):
module load BEDOPS