[ensembl-dev] Dev Digest, Vol 57, Issue 1

[Jamie Allen]

Hi Wallace,

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.

Cheers,
Jamie.

> On 16 Feb 2024, at 11:02, Wallace Ko <myko at l3-bioinfo.com> wrote:
> 
> Hi Jamie,
> 
> I am just wondering if the gnomAD v2 genome dataset itself is not included due to problems/limitations within the dataset itself.
> 
> 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.
> 
> Regards,
> Wallace Ko
> 
> 
> On Fri, Feb 16, 2024 at 4:38 PM Jamie Allen <jma at ebi.ac.uk <mailto:jma at ebi.ac.uk>> wrote:
>> Hi Wallace,
>> 
>> 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? 
>> 
>> Cheers,
>> Jamie.
>> 
>> > On 14 Feb 2024, at 12:00, dev-request at ensembl.org <mailto:dev-request at ensembl.org> wrote:
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>> >   1. gnomAD v2 genomes AF not included in VEP result or Ensembl
>> >      website (Wallace Ko)
>> > 
>> > 
>> > ----------------------------------------------------------------------
>> > 
>> > Message: 1
>> > Date: Wed, 14 Feb 2024 18:43:50 +0800
>> > From: Wallace Ko <myko at l3-bioinfo.com <mailto:myko at l3-bioinfo.com>>
>> > To: Ensembl developers list <dev at ensembl.org <mailto:dev at ensembl.org>>
>> > Subject: [ensembl-dev] gnomAD v2 genomes AF not included in VEP result
>> >       or Ensembl website
>> > Message-ID:
>> >       <CA+DTqFeFeNTzNM6=nVY82-YeheXuRev9547y0crxJntF=LiQ4A at mail.gmail.com <mailto:LiQ4A at mail.gmail.com>>
>> > Content-Type: text/plain; charset="utf-8"
>> > 
>> > Hi,
>> > 
>> > I notice that both VEP result and Ensembl website only include exomes AF
>> > from gnomAD v2.1.1. Could you explain why those from genomes of v2.1.1 are
>> > not included?
>> > 
>> > Regards,
>> > Wallace Ko
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>> > End of Dev Digest, Vol 57, Issue 1
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