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

Tool:    bedtools pairtobed (aka pairToBed)
Version: v2.31.1
Summary: Report overlaps between a BEDPE file and a BED/GFF/VCF file.

Usage:   bedtools pairtobed [OPTIONS] -a <bedpe> -b <bed/gff/vcf>

Options: 
	-abam	The A input file is in BAM format.  Output will be BAM as well. Replaces -a.
		- Requires BAM to be grouped or sorted by query.

	-ubam	Write uncompressed BAM output. Default writes compressed BAM.

		is to write output in BAM when using -abam.

	-bedpe	When using BAM input (-abam), write output as BEDPE. The default
		is to write output in BAM when using -abam.

	-ed	Use BAM total edit distance (NM tag) for BEDPE score.
		- Default for BEDPE is to use the minimum of
		  of the two mapping qualities for the pair.
		- When -ed is used the total edit distance
		  from the two mates is reported as the score.

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

	-s	Require same strandedness when finding overlaps.
		Default is to ignore stand.
		Not applicable with -type inspan or -type outspan.

	-S	Require different strandedness when finding overlaps.
		Default is to ignore stand.
		Not applicable with -type inspan or -type outspan.

	-type 	Approach to reporting overlaps between BEDPE and BED.

		either	Report overlaps if either end of A overlaps B.
			- Default.
		neither	Report A if neither end of A overlaps B.
		both	Report overlaps if both ends of A overlap  B.
		xor	Report overlaps if one and only one end of A overlaps B.
		notboth	Report overlaps if neither end or one and only one 
			end of A overlap B.  That is, xor + neither.

		ispan	Report overlaps between [end1, start2] of A and B.
			- Note: If chrom1 <> chrom2, entry is ignored.

		ospan	Report overlaps between [start1, end2] of A and B.
			- Note: If chrom1 <> chrom2, entry is ignored.

		notispan	Report A if ispan of A doesn't overlap B.
				- Note: If chrom1 <> chrom2, entry is ignored.

		notospan	Report A if ospan of A doesn't overlap B.
				- Note: If chrom1 <> chrom2, entry is ignored.

Refer to the BEDTools manual for BEDPE format.

