<html><head><meta http-equiv="content-type" content="text/html; charset=utf-8"></head><body style="overflow-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;">Hi Wallace,<div><br></div><div>Ah I see! No the set wasn’t excluded because of any technical issues that I am aware of, but purely because the much larger v3 set was on the way.</div><div><br></div><div>Cheers,</div><div>Jamie.<br id="lineBreakAtBeginningOfMessage"><div><br><blockquote type="cite"><div>On 16 Feb 2024, at 11:02, Wallace Ko <myko@l3-bioinfo.com> wrote:</div><br class="Apple-interchange-newline"><div><div dir="ltr">Hi Jamie,<div><br></div><div>I am just wondering if the gnomAD v2 genome dataset itself is not included due to problems/limitations within the dataset itself.<br><div><br></div><div>I am asked to implement an annotation of total AF from gnomAD v2 (i.e. sum of AC of exome and genome, divided by sum of AN of exome and genome). If the v2 genome dataset is being excluded from Ensembl/VEP due to problems/limitations of the dataset itself, we might need to review the practice of using the total AF.</div><div><br clear="all"><div><div dir="ltr" class="gmail_signature" data-smartmail="gmail_signature"><div dir="ltr">Regards,<div>Wallace Ko</div></div></div></div><br></div></div></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Fri, Feb 16, 2024 at 4:38 PM Jamie Allen <<a href="mailto:jma@ebi.ac.uk">jma@ebi.ac.uk</a>> wrote:<br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">Hi Wallace,<br>
<br>
Thanks for your query. Yes you’re correct we didn’t move the genomes to v2.1.1, as we were soon moving to the v3 set which has far more genome samples included. Is there a specific variant you’re looking at that is lacking population frequency information that is only in the gnomADv2.1.1 genomes set? <br>
<br>
Cheers,<br>
Jamie.<br>
<br>
> On 14 Feb 2024, at 12:00, <a href="mailto:dev-request@ensembl.org" target="_blank">dev-request@ensembl.org</a> wrote:<br>
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> 1. gnomAD v2 genomes AF not included in VEP result or Ensembl<br>
> website (Wallace Ko)<br>
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> ----------------------------------------------------------------------<br>
> <br>
> Message: 1<br>
> Date: Wed, 14 Feb 2024 18:43:50 +0800<br>
> From: Wallace Ko <<a href="mailto:myko@l3-bioinfo.com" target="_blank">myko@l3-bioinfo.com</a>><br>
> To: Ensembl developers list <<a href="mailto:dev@ensembl.org" target="_blank">dev@ensembl.org</a>><br>
> Subject: [ensembl-dev] gnomAD v2 genomes AF not included in VEP result<br>
> or Ensembl website<br>
> Message-ID:<br>
> <CA+DTqFeFeNTzNM6=nVY82-YeheXuRev9547y0crxJntF=<a href="mailto:LiQ4A@mail.gmail.com" target="_blank">LiQ4A@mail.gmail.com</a>><br>
> Content-Type: text/plain; charset="utf-8"<br>
> <br>
> Hi,<br>
> <br>
> I notice that both VEP result and Ensembl website only include exomes AF<br>
> from gnomAD v2.1.1. Could you explain why those from genomes of v2.1.1 are<br>
> not included?<br>
> <br>
> Regards,<br>
> Wallace Ko<br>
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