## Matching genomic regions / Overlap BEDPE with BED

### Description

Report overlaps between a BEDPE file and a BED/GFF/VCF file.

### Parameters

- File A is BAM format (yes, no) [no]
- Write uncompressed BAM output (yes, no) [no]
- When using BAM input, write output as BEDPE (yes, no) [no]
- Use BAM total edit distance for BEDPE score (yes, no) [no]
- Minimum overlap (0.0-1.0) [0.000000001]
- Force strandedness (yes, no) [no]
- Approach to reporting overlaps (either, neither, both, xor, notboth, ispan, ospan, notispan, notospan) [either]

### Details

pairToBed compares each end of a BEDPE feature or a paired-end BAM alignment to a feature file in search of overlaps.

NOTE: pairToBed requires that the BAM file is sorted/grouped by the read name. This allows pairToBed to extract correct alignment coordinates for each end based on their respective CIGAR strings. It also assumes that the alignments for a given pair come in groups of twos. There is not yet a standard method for reporting multiple alignments using BAM. pairToBed will fail if an aligner does not report alignments in pairs.

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 either a BEDPE file or a compressed or uncompressed BAM file depending on input file and options selected.

### 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.