Overview and use cases
http://bedtools.readthedocs.org/en/latest/content/bedtools-suite.html
bedtools intersect
http://bedtools.readthedocs.org/en/latest/content/tools/intersect.html
bedtools multicov
http://bedtools.readthedocs.org/en/latest/content/tools/multicov.html
bedtools merge
http://bedtools.readthedocs.org/en/latest/content/tools/merge.html