snpEff assigned all variants as modifier intergenic

Question

[misterie]

Hi!

I have following problem:

I have used a snpEff for annotation my VCF files. I created database (I have a custom gff and reference genome). Every time snpEff detect all my snps as a intergenic (modifier). It is not true. Sth is wrong, but I do not know what.

Can you help me? Any suggestions?

Thank you in advance.

[Pierre Lindenbaum]

show us a line of the VCF and the corresponding overlapping entries in the GFF

[misterie]

Now I compared all files. The 1st chromosome is annotated fine, but other are not. In 1st chromosome I have many types of snp localisations, but in other all snps are intergenic...

[misterie]

I see the problem is during building a database...

Look here:

Reading sequence '1', length: 158534110
Adding genomic sequences to exons:  Done (1857 sequences added, 0 ignored).
Reading sequence '2', length: 136231102
Adding genomic sequences to exons:  Done (0 sequences added, 0 ignored).
Reading sequence '3', length: 121005158
Adding genomic sequences to exons:  Done (0 sequences added, 0 ignored).
Reading sequence '4', length: 120000601
Adding genomic sequences to exons:  Done (0 sequences added, 0 ignored).
Reading sequence '5', length: 120089316
Adding genomic sequences to exons:  Done (0 sequences added, 0 ignored).
Reading sequence '6', length: 117806340
Adding genomic sequences to exons:  Done (0 sequences added, 0 ignored).
Reading sequence '7', length: 110682743
Adding genomic sequences to exons:  Done (0 sequences added, 0 ignored).
Reading sequence '8', length: 113319770
Adding genomic sequences to exons:  Done (0 sequences added, 0 ignored).
Reading sequence '9', length: 105454467
Adding genomic sequences to exons:  Done (0 sequences added, 0 ignored).
Reading sequence '10', length: 103308737
Adding genomic sequences to exons:  Done (0 sequences added, 0 ignored).

[aaron.phillips]

Hey misterie, did you fix this issue? I am having the same problem and have not been able to find a solution yet.

[bioblast]

I was getting the same error, so I used an abbreviated gff that contained focal regions I am interested in (CDS regions of our target genes), and found that this worked. However, this seems like a pretty hacky fix that may not be sufficient for most people interested in the genome as a whole.