[ensembl-dev] Asking help for incorrect VEP results

[Andrew Parton]

Hi,

I’ve had a look at this issue this morning and I’m unable to reproduce this error. If I run VEP with the command:

`perl vep -id '15 89582890 . C G' —database`

Then VEP returns 4 overlapping transcripts over 3 genes. 2 of the consequences returned are missense_variant, and for each of these the codon change is Cgt/Ggt, corresponding to a genomic location of 89582890-89582892 for the ORF as expected.

If you’re still seeing this issue, could you please send me your VEP input command and your full output?

Kind Regards,
Andrew

> On 26 Oct 2020, at 06:24, 孙怀远 <sunhy at mail.cbi.pku.edu.cn> wrote:
> 
> Hi,
> 
> 
> 
> I'm a PhD candidate from Ge Gao's group. When using VEP, I found SNPs predicted to be missense variants, but the ORF was annotated incorrectly. For example, the ORF of a SNP on chr15:89582890 is 89582890-89582892 in gencode.v34, but annotated to be 89582890-89582888 in reverse strand. Please help me correct these annotations. The VEP version I used is v100.3.
> 
> 
> 
> Thank you!
> 
> 
> 
> Huaiyuan Sun
> 
> 
> 
> 
> Huaiyuan Sun Ph.D. candidate
> Peking-Tsinghua Center for Life Sciences 
> Peking University, Beijing 100871, China
> Tel: 18810504686
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