BEDOPS, a software suite for common genomic analysis tasks which offers improved flexibility, scalability and execution time characteristics over previously 
published packages. The suite includes a utility to compress large inputs into a lossless format that can provide greater space savings and faster data extractions than alternatives.
Finding relationships between two or more genomic datasets is an important problem. As an example, one might want to know how much overlap exists between the elements of two datasets, to quantitatively establish the degree to which they are similar.
Another need is to merge or filter elements. For example, retrieving non-overlapping, “unique” elements from multiple BED files.
The bedops program offers several Boolean set and multiset operations, including union, subset, and difference, to assist investigators with answering these types of questions. Importantly, bedops handles any number of any-size inputs at once when computing results in order to maximize efficiency.
One can also use bedops to symmetrically or asymmetrically pad coordinates.
BEDOPS can be downloaded from here
Reference:
Neph S, Kuehn MS, Reynolds AP, Haugen E, Thurman RE, Johnson AK, Rynes E, Maurano MT, Vierstra J, Thomas S, Sandstrom R, Humbert R, Stamatoyannopoulos JA. BEDOPS: high-performance genomic feature operations. Bioinformatics. 2012 Jul 15;28(14):1919-20. Epub 2012 May 9. PubMed PMID: 22576172;
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