overlaps between subfeatures in the underlying annotation

Question

[Ric]

Hi, I currently use FeatureSequence.

Unfortunately, it does not work correctly with [*the presence of overlaps between subfeatures in the underlying annotation. Overlapping subfeatures are fundamentally problematic for this program, and that's unlikely to change. I couldn't find a way to consistently and correctly highlight/hide/etc overlapping subfeatures without a bunch of extra logic and headaches regarding the different possibilities inherent with nested boundaries.*](https://github.com/twsaari/FeatureSequence/issues/14#issuecomment-452476971)

Is there any other online tool available which can handle overlaps or is there a way to fix the overlaps inside the annotation file?

[lieven.sterck]

you can try to run agat , this can process a GFF file and do lots of things with it, such as merging overlapping features in the annotation.

AGAT - Another Gff/Gtf Analysis Toolkit