[ensembl-dev] Asking help for incorrect VEP results

[孙怀远]

Hi,

Thanks for your reply. I've checked in gencode.v34, the codon at location 89582890-89582892 should be CGT and the variant change it to TGT. The output of VEP showed the codon as Ggt/Agt, which is corresponding to bases in 89582888-89582890 (AGC) in reverse strand. I assume the correct output should be Cgt/Tgt.


Huaiyuan 


> -----原始邮件-----
> 发件人: "Andrew Parton" <aparton at ebi.ac.uk>
> 发送时间: 2020-10-26 23:58:03 (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,
> 
> Thank you for sending on your input/output data. The output that you’ve sent matches with your initial assertion that the overlapping codon should be at location 89582890-89582892. Both transcripts with missense_variant consequences are on the forward strand with the first base within the codon being altered by the variant.
> 
> Could you please give me more details about why you believe the ORF is incorrect, and what you would expect to see here?
> 
> Kind Regards,
> Andrew
> 
> > On 26 Oct 2020, at 13:21, 孙怀远 <sunhy at mail.cbi.pku.edu.cn> wrote:
> > 
> > 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
> >>> _______________________________________________
> >>> Dev mailing list    Dev at ensembl.org
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> >> 
> >> 
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> 
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