A flexible suite of utilities for comparing genomic features
The BEDTools utilities allow one to address common genomics tasks such as finding feature overlaps and computing coverage. The utilities are largely based on four widely-used file formats: BED, GFF/GTF, VCF, and SAM/BAM. Using BEDTools, one can develop sophisticated pipelines that answer complicated research questions by "streaming" several BEDTools together.
Also note that pybedtools, the Python extension of BEDTools, has been published in Bioinformatics. It extends upon much of the functionality in BEDTools and provides a very powerful and flexible Python interface for manipulating and comparing genomic features in BED/VCF/GFF/GTF/SAM/BAM format.