snpEff assigned all variants as modifier intergenic
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.
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show us a line of the VCF and the corresponding overlapping entries in the GFF
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...
I see the problem is during building a database...
Look here:
Hey misterie, did you fix this issue? I am having the same problem and have not been able to find a solution yet.
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.