[ensembl-dev] New VEP endpoint

[Andrew Parton]

Hi,

Gnomad exome is used for the VEP endpoint. REST VEP relies on a cache, and as such has associated limitations as outlined here: https://www.ensembl.org/info/docs/tools/vep/script/vep_cache.html#cache <https://www.ensembl.org/info/docs/tools/vep/script/vep_cache.html#cache>. 

The populations that show up in the VEP endpoint are the ones isolated using the VEP flags —af_gnomad and —af_1kg as defined in https://www.ensembl.org/info/docs/tools/vep/script/vep_options.html <https://www.ensembl.org/info/docs/tools/vep/script/vep_options.html#basic>. Currently, the ALL population is not included, however this is an idea worth considering for a future release. Thank you for the suggestion.

Kind Regards,
Andrew

> On 18 Jul 2018, at 10:53, Wolf Beat <Beat.Wolf at hefr.ch> wrote:
> 
> Thank you for the fast response.
> 
> 
> There are two questions i still have:
> 
> Is gnomad exome or genome used for the VEP endpoint?
> 
> How are the populations selected that show up in the VEP endpoint? Or to be specific, why is the ALL population not part of it?
> 
> 
> Kind regards
> 
> Beat Wolf
> 
> ________________________________
> From: Dev <dev-bounces at ensembl.org> on behalf of Andrew Parton <aparton at ebi.ac.uk>
> Sent: Wednesday, July 18, 2018 11:28:25 AM
> To: Ensembl developers list
> Subject: Re: [ensembl-dev] New VEP endpoint
> 
> Hi,
> 
> Thank you for your query. Population data can be taken form the REST API using the /variation/species/ID endpoint.
> 
> For example, for the rsID contained in your email, you can access population data with the URL http://rest.ensembl.org/variation/human/rs58651353?content-type=application/json;pops=1
> 
> If there’s anything else that we can do to help, please don’t hesitate to ask.
> 
> Kind Regards,
> Andrew
> 
> On 18 Jul 2018, at 10:11, Wolf Beat <Beat.Wolf at hefr.ch<mailto:Beat.Wolf at hefr.ch>> wrote:
> 
> Hello,
> 
> 
> I was wondering, with the new VEP endpoint is there a way to get the "ALL" population from 100 genomes, gnomad etc.?
> 
> Its also unclear to me if the gnomad exome or genome frequency is used.
> 
> 
> In short, is there a way to get the same information that is present on the webpage under population genetics (like http://www.ensembl.org/Homo_sapiens/Variation/Population?db=core;r=2:178751544-178752544;v=rs58651353;vdb=variation;vf=11676771#1000genomesprojectphase3_anchor ) out of the ensembl REST endpoint? Right now it seems that there is much more information on the webpage.
> 
> 
> To be clear, i don't actually need all the information on the webpage, all i actually need is the "ALL" population. But the fact that the webpage and the vep rest endpoint does not have the same information makes me think that something is missing.
> 
> 
> Kind regards
> 
> 
> Beat Wolf
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