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.
- 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
To see what other modules are needed, what commands are available and how to get additional help type
module help bedops
To see what versions of Bedops are available type
module avail bedops
To use Bedops, include a command like this in your batch script or interactive session to load the Bedops module:
module load bedops
Be sure you also load any other modules needed, as listed by the
module help bedops command.