Question: snpEff assigned all variants as modifier intergenic
0
gravatar for bwczech
5 months ago by
bwczech60
bwczech60 wrote:

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.

snpeff ngs vcf • 321 views
ADD COMMENTlink written 5 months ago by bwczech60

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

ADD REPLYlink written 5 months ago by Pierre Lindenbaum119k

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...

ADD REPLYlink written 5 months ago by bwczech60

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).
ADD REPLYlink modified 5 months ago by finswimmer11k • written 5 months ago by bwczech60
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