[ensembl-dev] Asking help for incorrect VEP results

[Andrew Parton]

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
>>> Posting guidelines and subscribe/unsubscribe info: https://lists.ensembl.org/mailman/listinfo/dev_ensembl.org
>>> Ensembl Blog: http://www.ensembl.info/
>> 
>> 
>> _______________________________________________
>> Dev mailing list    Dev at ensembl.org
>> Posting guidelines and subscribe/unsubscribe info: https://lists.ensembl.org/mailman/listinfo/dev_ensembl.org
>> Ensembl Blog: http://www.ensembl.info/
> _______________________________________________
> Dev mailing list    Dev at ensembl.org
> Posting guidelines and subscribe/unsubscribe info: https://lists.ensembl.org/mailman/listinfo/dev_ensembl.org
> Ensembl Blog: http://www.ensembl.info/