## Matching genomic regions / Intersect BED

### Description

Report overlaps between two feature files.

### Parameters

- File A is BAM format (yes, no) [no]
- Write uncompressed BAM output (yes, no) [no]
- Write output as BED (yes, no) [no]
- Write the original entry in A for each overlap (yes, no) [no]
- Write the original entry in B for each overlap (yes, no) [no]
- Write the original A and B entries for overlapped A features (yes, no) [no]
- Write the original A and B entries for all A features (yes, no) [no]
- Write the original A entry once if any overlaps found in B (yes, no) [no]
- For each entry in A, report the number of overlaps with B (yes, no) [no]
- Only report those entries in A that have no overlaps with B (yes, no) [no]
- Minimum overlap required as a fraction of A (0.0-1.0) [0.000000001}
- Require that the fraction overlap be reciprocal for A and B (yes, no) [no]
- Force strandedness (yes, no) [no]
- Treat split BAM or BED12 entries as distinct BED intervals (yes, no) [no]

### Details

By far, the most common question asked of two sets of genomic features is whether or not any of the features in the two sets “overlap” with one another. This is known as feature intersection. intersectBed allows one to screen for overlaps between two sets of genomic features. Moreover, it allows one to have fine control as to how the intersections are reported. intersectBed works with both BED/GFF/VCF and BAM files as input.

Selecting "File A is BAM format [yes]" is analogous to using "-abam" option instead of "-a" in the command line version.

### Output

The output is a tab-delimited text 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.