[ensembl-dev] New VEP endpoint

Wolf Beat Beat.Wolf at hefr.ch
Wed Jul 18 10:53:07 BST 2018


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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