Matching genomic regions / Find overlapping regions
Given two BED files, this tool returns those regions which overlap with some region in the other input file. Also known as intersection.
- Type of regions returned (Original regions from file A, Original regions from file A augmented with info from file B, Original regions from both files, Regions from both files merged, Overlapping parts of the regions) [Original regions from file A]
- Minimum number of overlapping bases (1-1000000000) 
Note that if two A regions match one B region and you ask for "Original regions from both files", the B region will appear twice in the result list.
Output is a BED file.
This tool uses an in-house Java code.