Matching genomic regions / Remove overlapping regions
Given two BED files, this tool returns those regions from file A which do not have overlap with the regions in file B.
Also known as subtraction.
- Minimum number of overlapping bases (1-1000000000) 
The orignal, whole regions from file A are returned. If you allow some overlapping bases and would like to get only those parts of A regions which don't overlap, please use the tool "Subtract BED".
Output is a BED file.
This tool uses an in-house Java code.