<div dir="auto">I've sent unsubscription request a few times, yet I keep getting these emails. </div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">בתאריך יום ו׳, 21 בינו׳ 2022, 16:26, מאת Syed Hossain <<a href="mailto:snhossain@ebi.ac.uk">snhossain@ebi.ac.uk</a>>:<br></div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">On 2022-01-20 18:00, <a href="mailto:dev-request@ensembl.org" target="_blank" rel="noreferrer">dev-request@ensembl.org</a> wrote:<br>
> Send Dev mailing list submissions to<br>
> <a href="mailto:dev@ensembl.org" target="_blank" rel="noreferrer">dev@ensembl.org</a><br>
> <br>
> To subscribe or unsubscribe via the World Wide Web, visit<br>
> <a href="http://mail.ensembl.org/mailman/listinfo/dev_ensembl.org" rel="noreferrer noreferrer" target="_blank">http://mail.ensembl.org/mailman/listinfo/dev_ensembl.org</a><br>
> or, via email, send a message with subject or body 'help' to<br>
> <a href="mailto:dev-request@ensembl.org" target="_blank" rel="noreferrer">dev-request@ensembl.org</a><br>
> <br>
> You can reach the person managing the list at<br>
> <a href="mailto:dev-owner@ensembl.org" target="_blank" rel="noreferrer">dev-owner@ensembl.org</a><br>
> <br>
> When replying, please edit your Subject line so it is more specific<br>
> than "Re: Contents of Dev digest..."<br>
> <br>
> <br>
> Today's Topics:<br>
> <br>
> 1. Change in consequence and HGVSp between VEP v99 and v100<br>
> (Wallace Ko)<br>
> <br>
> <br>
> ----------------------------------------------------------------------<br>
> <br>
> Message: 1<br>
> Date: Thu, 20 Jan 2022 13:02:47 +0800<br>
> From: Wallace Ko <<a href="mailto:myko@l3-bioinfo.com" target="_blank" rel="noreferrer">myko@l3-bioinfo.com</a>><br>
> To: Ensembl developers list <<a href="mailto:dev@ensembl.org" target="_blank" rel="noreferrer">dev@ensembl.org</a>><br>
> Subject: [ensembl-dev] Change in consequence and HGVSp between VEP v99<br>
> and v100<br>
> Message-ID:<br>
> <<a href="mailto:CAMsJki0yY4PZG7sSYiNx-SkifAXrVcFsURgMKsZ3Q4Gz7ta_xg@mail.gmail.com" target="_blank" rel="noreferrer">CAMsJki0yY4PZG7sSYiNx-SkifAXrVcFsURgMKsZ3Q4Gz7ta_xg@mail.gmail.com</a>><br>
> Content-Type: text/plain; charset="utf-8"<br>
> <br>
> Hello Ensembl Team,<br>
> <br>
> During re-evaluation of some old samples, we found that VEP v99 and <br>
> v100<br>
> give the same HGVSc, but different annotation, including consequence <br>
> and<br>
> HGVSp, e.g.:<br>
> <br>
> 1. HGVSc: NM_001034954.1:c.182T>C<br>
> - v99:<br>
> - HGVSp: NP_001030126.1:p.Pro61=<br>
> - Consequence: synonymous_variant<br>
> - v100:<br>
> - HGVSp: NP_001030126.1:p.Leu61Pro<br>
> - Consequence: missense_variant<br>
> 2. HGVSc: NM_000283.3:c.928-9_940dup<br>
> - v99 HGVSp: NP_000274.2:p.Tyr314CysfsTer50<br>
> - v100 HGVSp: -<br>
> 3. HGVSc: NM_001040108.1:c.4243-36_4243-1dup<br>
> - v99 HGVSp:<br>
> <br>
> NP_001035197.1:p.Gln1414_Ile1415insHisIleAlaAsnTerSerTyrSerPhePheProTer<br>
> - v100 HGVSp: NP_001035197.1:p.Gln1414_Ile1415insHisIleAlaAsnTer<br>
> <br>
> I tried using offline VEP v100 with v99 cache and vice versa. VEP v100<br>
> produces the new results regardless of the cache being used. So it <br>
> should<br>
> be due to code change instead of data update.<br>
> <br>
> The change is sort of significant but there seem no relevant details in <br>
> the<br>
> release descriptions (<br>
> <a href="https://github.com/Ensembl/ensembl-vep/releases?q=release%2F100" rel="noreferrer noreferrer" target="_blank">https://github.com/Ensembl/ensembl-vep/releases?q=release%2F100</a>) or the<br>
> mail list about the change.<br>
> <br>
> I wonder what causes such changes and if there is a scope or pattern on <br>
> the<br>
> changes. Otherwise, we may need to re-analyze all results from VEP v99 <br>
> or<br>
> older.<br>
> <br>
> Thank you.<br>
> <br>
> Regards,<br>
> Wallace Ko<br>
> -------------- next part --------------<br>
> An HTML attachment was scrubbed...<br>
> URL:<br>
> <<a href="http://mail.ensembl.org/pipermail/dev_ensembl.org/attachments/20220120/011e8c23/attachment-0001.html" rel="noreferrer noreferrer" target="_blank">http://mail.ensembl.org/pipermail/dev_ensembl.org/attachments/20220120/011e8c23/attachment-0001.html</a>><br>
> <br>
> ------------------------------<br>
> <br>
> Subject: Digest Footer<br>
> <br>
> _______________________________________________<br>
> Dev mailing list <a href="mailto:Dev@ensembl.org" target="_blank" rel="noreferrer">Dev@ensembl.org</a><br>
> Posting guidelines and subscribe/unsubscribe info:<br>
> <a href="https://lists.ensembl.org/mailman/listinfo/dev_ensembl.org" rel="noreferrer noreferrer" target="_blank">https://lists.ensembl.org/mailman/listinfo/dev_ensembl.org</a><br>
> Ensembl Blog: <a href="http://www.ensembl.info/" rel="noreferrer noreferrer" target="_blank">http://www.ensembl.info/</a><br>
> <br>
> <br>
> ------------------------------<br>
> <br>
> End of Dev Digest, Vol 35, Issue 1<br>
> **********************************<br>
<br>
Hello Wallace,<br>
<br>
Thank you for reporting this issue. But, unfortunately, we were unable <br>
to reproduce it.<br>
<br>
For our case VEP v99 is also giving the same output as what you get for <br>
VEP v100 (i.e - HGVSc: NM_001034954.1:c.182T>C --> HGVSp: <br>
NP_001030126.1:p.Leu61Pro).<br>
<br>
Can you kindly share the full command you are using and (if possible) <br>
the input files.<br>
<br>
Best regards,<br>
Nakib<br>
<br>
_______________________________________________<br>
Dev mailing list <a href="mailto:Dev@ensembl.org" target="_blank" rel="noreferrer">Dev@ensembl.org</a><br>
Posting guidelines and subscribe/unsubscribe info: <a href="https://lists.ensembl.org/mailman/listinfo/dev_ensembl.org" rel="noreferrer noreferrer" target="_blank">https://lists.ensembl.org/mailman/listinfo/dev_ensembl.org</a><br>
Ensembl Blog: <a href="http://www.ensembl.info/" rel="noreferrer noreferrer" target="_blank">http://www.ensembl.info/</a><br>
</blockquote></div>