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

Tool:    bedtools window (aka windowBed)
Version: v2.31.1
Summary: Examines a "window" around each feature in A and
	 reports all features in B that overlap the window. For each
	 overlap the entire entry in A and B are reported.

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

Options: 
	-abam	The A input file is in BAM format.  Output will be BAM as well. Replaces -a.

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

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

	-w	Base pairs added upstream and downstream of each entry
		in A when searching for overlaps in B.
		- Creates symmetrical "windows" around A.
		- Default is 1000 bp.
		- (INTEGER)

	-l	Base pairs added upstream (left of) of each entry
		in A when searching for overlaps in B.
		- Allows one to define asymmetrical "windows".
		- Default is 1000 bp.
		- (INTEGER)

	-r	Base pairs added downstream (right of) of each entry
		in A when searching for overlaps in B.
		- Allows one to define asymmetrical "windows".
		- Default is 1000 bp.
		- (INTEGER)

	-sw	Define -l and -r based on strand.  For example if used, -l 500
		for a negative-stranded feature will add 500 bp downstream.
		- Default = disabled.

	-sm	Only report hits in B that overlap A on the _same_ strand.
		- By default, overlaps are reported without respect to strand.

	-Sm	Only report hits in B that overlap A on the _opposite_ strand.
		- By default, overlaps are reported without respect to strand.

	-u	Write the original A entry _once_ if _any_ overlaps found in B.
		- In other words, just report the fact >=1 hit was found.

	-c	For each entry in A, report the number of overlaps with B.
		- Reports 0 for A entries that have no overlap with B.
		- Overlaps restricted by -w, -l, and -r.

	-v	Only report those entries in A that have _no overlaps_ with B.
		- Similar to "grep -v."

	-header	Print the header from the A file prior to results.

