[ensembl-dev] Asking help for incorrect VEP results

[孙怀远]

Thanks for your reply. I used the download version of VEP, my command is:
vep -i input.txt --offline --stats_text --force_overwrite -o out.txt

My input format is: 
15      89582890        89582890        C/T     -       SNP599326

My output:
SNP599326       15:89582890     T       ENSG00000140534 ENST00000268138 Transcript      missense_variant        977     859     287     G/S     Ggt/Agt -       IMPACT=MODERATE;STRAND=1
SNP599326       15:89582890     T       ENSG00000259713 ENST00000559041 Transcript      intron_variant,non_coding_transcript_variant    -       -       -       -       -       -       IMPACT=MODIFIER;STRAND=1
SNP599326       15:89582890     T       ENSG00000259615 ENST00000560477 Transcript      upstream_gene_variant   -       -       -       -       -       -       IMPACT=MODIFIER;DISTANCE=593;STRAND=-1
SNP599326       15:89582890     T       ENSG00000140534 ENST00000560985 Transcript      missense_variant        859     859     287     G/S     Ggt/Agt -       IMPACT=MODERATE;STRAND=1


> -----原始邮件-----
> 发件人: "Andrew Parton" <aparton at ebi.ac.uk>
> 发送时间: 2020-10-26 18:04:45 (星期一)
> 收件人: "Ensembl developers list" <dev at ensembl.org>
> 抄送: gaog <gaog at mail.cbi.pku.edu.cn>
> 主题: Re: [ensembl-dev] Asking help for incorrect VEP results
> 
> 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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> 
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