## Matching genomic regions / Compare two BEDPE files

### Description

Report overlaps between two paired-end BED files (BEDPE).

### Parameters

- Minimum overlap (0.0-1.0) [0.000000001]
- Approach to reporting overlaps (either, neither, both) [both]
- Ignore strands when searching for overlaps (yes, no) [no]
- Require different names (yes, no) [no]
- Add slop (yes, no) [no]
- The amount of slop in bp to be added to each footprint (Integer) [0]
- Add slop based to each BEDPE footprint based on strand (yes, no) [no]

### Details

pairToPair compares two BEDPE files in search of overlaps where each end of a BEDPE feature in A overlaps with the ends of a feature in B. For example, using pairToPair, one could screen for the exact same discordant paired-end alignment in two files. This could suggest (among other things) that the discordant pair suggests the same structural variation in each file/sample.

### Output

The output is a BEDPE file.

### References

This tool uses the BEDTools package. Please cite the article:

Quinlan AR and Hall IM, 2010. BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics. 26, 6, pp. 841–842.

Please see the BEDTools homepage for more details.