bedtools groupby is a useful tool that mimics the “group by” clause in database systems. Given a file or stream that is sorted by the appropriate “grouping columns” (-g), groupby will compute summary statistics on another column (-c) in the file or stream. This will work with output from all BEDTools as well as any other tab-delimited file or stream. As such, this is a generally useful tool for all command-line analyses, not just genomics related research.