multiBamCov (BAM) Counts sequence coverage for multiple position-sorted bams at specific loci defined in a BED/GFF/VCF file BedTools

multiBamCov will report a count of alignments for each BAM at each  interval

Program: multiBamCov (v2.14.2)
Summary: Counts sequence coverage for multiple bams at specific loci.

Usage:   multiBamCov [OPTIONS] -bams aln.1.bam aln.2.bam ... aln.n.bam -bed

Options:
        -bams   The bam files.

        -bed    The bed file.

        -q      Minimum mapping quality allowed. Default is 0.

        -D      Include duplicate-marked reads.  Default is to count non-duplicates only

        -F      Include failed-QC reads.  Default is to count pass-QC reads only

        -p      Only count proper pairs.  Default is to count all alignments with MAPQ
                greater than the -q argument, regardless of the BAM FLAG field.
 

 the sample output looks like

  chr20 0 100000 19312 16844
  chr20 100000 200000 43910 37579
  chr20 200000 300000 43245 43215
  chr20 300000 400000 41653 47556
  chr20 400000 500000 42929 43165
  chr20 500000 600000 44265 45325 

The last two columns are the count  of alignments in the first and second BAM, respectively.