The General Feature Format is a widely used format for annotating genome sequences. If indexed with tabix, gff files can be viewed in IGV or elsewhere. While features are organized in a nested manner (e.g. genes > exons > variant), you can pull out the individual types and index them, or combine only a few for viewing in your genome browser.

I was working with wormbase annotation files, which combine all the different types of features together (genes, ncRNA, mRNA, binding site, operon, G Quartets, piRNAs, etc). This results in a very dense track in IGV which makes it difficult to disentangle what role individual features (or features of interest) might have.

As a result, I wrote this very short script for splitting the individual feature types apart, sorting them, and indexing them with tabix. This way they can be selectively viewed in IGV or elsewhere.