How to merge two gff3 files?

Question

[Raito92]

Hello everyone, I'm looking for a script or a tool able to merge two gff3 files, made as follows:

1) A file containing annotation data for my species

2) Another file with additional annotation (information obtained later, trying to annotate the genome against another organism in order to give a function to more genes)

The coordinate system of the two gff3s is the same since both the gff3s are produced starting from the genome of my species of interest.

Anything I found seems to be outdated, thanks in advance for your help!

Answer 1

[lieven.sterck]

I use AGAT for that and many other GFF processing things as well.

AGAT - Another Gff Analysis Toolkit

[Raito92]

Hi, thanks for your answer, what script do you use exactly?

agat_sp_merge_annotations.pl ?

[lieven.sterck]

depends on what exactly you want to achieve but yes, agat_sp_merge_annotations.pl sounds about right.

alternatively you can first cat both gff files together and then run agat_convert_sp_gxf2gxf.pl to fix the 'issues' .

On their github page there are lots of explanations and guidelines on what to use when. There are likely also different routes that lead to the same result.