GFF reformator

Question

[HERMAN]

Hi Biostars,

Is there a tool out there that can take any gff and ensure that each occurence of a CDS / mRNA / gene is part of the " three-level gene " structure ( http://gmod.org/wiki/GFF3 ) ? I have a bunch of very poorly annotated gff annotations that only have CDS features to represent protein-coding genes.

I started to code a " parser " myself but this appears to be more complicated than I thought at first glance.

Thank you for your time, Simon

Answer 1

[GenoMax]

Take a look at AGAT toolkit for all things related to GTF/GFF: https://github.com/NBISweden/AGAT

[HERMAN]

Thank you very much, I always overlook this suite. Looks like I shouldn't !