```bash
docker run --rm quay.io/biocontainers/bedtools:2.31.1--h13024bc_3 bedtools pairtopair -h
```

Tool:    bedtools pairtopair (aka pairToPair)
Version: v2.31.1
Summary: Report overlaps between two paired-end BED files (BEDPE).

Usage:   bedtools pairtopair [OPTIONS] -a <BEDPE> -b <BEDPE>

Options: 
	-f	Minimum overlap required as fraction of A (e.g. 0.05).
		Default is 1E-9 (effectively 1bp).

	-type 	Approach to reporting overlaps between A and B.

		neither	Report overlaps if neither end of A overlaps B.
		either	Report overlaps if either ends of A overlap B.
		both	Report overlaps if both ends of A overlap B.
		notboth	Report overlaps if one or neither of A's overlap B.
		- Default = both.

	-slop 	The amount of slop (in b.p.). to be added to each footprint of A.
		*Note*: Slop is subtracted from start1 and start2
			and added to end1 and end2.

		- Default = 0.

	-ss	Add slop based to each BEDPE footprint based on strand.
		- If strand is "+", slop is only added to the end coordinates.
		- If strand is "-", slop is only added to the start coordinates.
		- By default, slop is added in both directions.

	-is	Ignore strands when searching for overlaps.
		- By default, strands are enforced.

	-rdn	Require the hits to have different names (i.e. avoid self-hits).
		- By default, same names are allowed.

Refer to the BEDTools manual for BEDPE format.

