Hi all,

I have a set of SNPs for an organism for which annotation is still in progress. I obtained set of SNPs of interest and to get functional information I have GFF file with genes predicted by Augustus and GFF3 file with proteins annotation from InterProScan. Is there any tool that would let me integrate this information or will I be forced to write my own script? I didn't manage to find what I need so far but maybe I'm missing something.

So far I annotated my SNPs with augustus GFF file using snpEff but I can't do the same with InterProScan GFF3 file as I am having more or less this kind of output of building database for my organism:

Reading GFF3 data file : 'path_to_file' Total: 0 markers added.

Create exons from CDS (if needed): 
Exons created for 0 transcripts.

Deleting redundant exons (if needed): 
    Total transcripts with deleted exons: 0

Collapsing zero length introns (if needed): 
    Total collapsed transcripts: 0
Reading sequences   :
Reading FASTA file: 'path_to_reference'
    Reading sequence 'scf_1', length: 2205567
    Adding genomic sequences to exons:  Done (0 sequences added, 0 ignored).
    Reading sequence 'scf_2', length: 1244474
    Adding genomic sequences to exons:  Done (0 sequences added, 0 ignored).
    Reading sequence 'scf_3', length: 1199189
    Adding genomic sequences to exons:  Done (0 sequences added, 0 ignored).
    Reading sequence 'scf_4', length: 3287760
    Adding genomic sequences to exons:  Done (0 sequences added, 0 ignored).

And later on:

Total: 0 sequences added, 0 sequences ignored.
Adjusting transcripts: 
Adjusting genes: 
Adjusting chromosomes lengths: 
Ranking exons: 
Create UTRs from CDS (if needed): 
Correcting exons based on frame information.

Remove empty chromosomes: 
    Removing empty chromosome: 'g4789.t1'
    Removing empty chromosome: 'g7757.t1'
    Removing empty chromosome: 'g5919.t1'

It's the same for all scaffolds and genes - it looks to me like my genes are treated as chromosomes. How could I use this GFF3 file to biuld snpEff database for the annotation?

Regards, Agata