In two different projects I need to modify annotation files. For instance I need to split a gene into two independent ones following evidence that they are separate transcriptional units. I also need to create a new alternative isoform of a gene with a longer 3′UTR. The source file for the annotations are in GFF or GTF format and the only tools that I can think about are emacs or vim. But isn't there a better tool, that would automagically take care that the gene, transcript and parent IDs stay consistent?