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

Tool:    bedtools multicov (aka multiBamCov)
Version: v2.31.1
Summary: Counts sequence coverage for multiple bams at specific loci.

Usage:   bedtools multicov [OPTIONS] -bams aln.1.bam aln.2.bam ... aln.n.bam -bed <bed/gff/vcf>

Options: 
	-bams	The bam files.

	-bed	The bed file.

	-split	Treat "split" BAM or BED12 entries as distinct BED intervals.

	-s	Require same strandedness.  That is, only report hits in B
		that overlap A on the _same_ strand.
		- By default, overlaps are reported without respect to strand.

	-S	Require different strandedness.  That is, only report hits in B
		that overlap A on the _opposite_ strand.
		- By default, overlaps are reported without respect to strand.

	-f	Minimum overlap required as a fraction of each -bed record.
		- Default is 1E-9 (i.e., 1bp).
		- FLOAT (e.g. 0.50)

	-r	Require that the fraction overlap be reciprocal for each -bed and B.
		- In other words, if -f is 0.90 and -r is used, this requires
		  that B overlap 90% of each -bed and the -bed record _also_ overlaps 90% of B.

	-q	Minimum mapping quality allowed. Default is 0.

	-D	Include duplicate reads.  Default counts non-duplicates only

	-F	Include failed-QC reads.  Default counts pass-QC reads only

	-p	Only count proper pairs.  Default counts all alignments with
		MAPQ > -q argument, regardless of the BAM FLAG field.

