What it does
bedtools multicov, reports the count of alignments from multiple position-sorted and indexed BAM files that overlap intervals in a BED file. Specifically, for each BED interval provided, it reports a separate count of overlapping alignments from each BAM file.
This tool is part of the bedtools package from the Quinlan laboratory.
Citation
If you use this tool in Galaxy, please cite:
Bjoern A. Gruening (2014), Galaxy wrapper