What it does
bedtools annotate, well, annotates one BED/bedGraph/GFF/VCF/EncodePeak file with the coverage and number of overlaps observed from multiple other BED/bedGraph/GFF/VCF/EncodePeak files. In this way, it allows one to ask to what degree one feature coincides with multiple other feature types with a single command.
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