Collectively, the bedtools utilities are a swiss-army knife of tools
for a wide-range of genomics analysis tasks. The most widely-used
tools enable genome arithmetic: that is, set theory on the genome. For
example, bedtools allows one to intersect, merge, count, complement,
and shuffle genomic intervals from multiple files in widely-used
genomic file formats such as BAM, BED, GFF/GTF, VCF. 

While each individual tool is designed to do a relatively simple task
(e.g., intersect two interval files), quite sophisticated analyses can
be conducted by combining multiple bedtools operations on the UNIX
command line.