[ensembl-dev] REST service

[Wolf Beat]

A quick follow up question to my last email, as i'm still trying to figure out how to use the rest interface.


So, maybe for context, all i want is basically the information on the ensembl website that tells me the maf in the general population.

ideally that information would be included in the "overlap" endpoint, as that is how i'm identifying a variant in the first place, but i'm ok with querying a second time.


Anyway, i'm trying to understand when what values are returned by the endpoint, and i can't seem to find a system.


What i now discovered is that for some reason deletions have their maf numbers reported in a strange format:

An example can be found here:

http://grch37.rest.ensembl.org/vep/hsapiens/id/rs58651353?ExAC=1&distance=0&content-type=application/json


So the maf numbers suddenly have a "-:" in front of them. I don't see why.

I also seem to have a lot of insertion which should have maf values associated, which do not have them in the rest interface:

http://grch37.rest.ensembl.org/vep/hsapiens/id/rs142807316?ExAC=1&distance=0&content-type=application/json


Looking at the website you can see that this variant is supposed to have a maf value:

http://grch37.ensembl.org/Homo_sapiens/Variation/Explore?r=5:155770922-155771921;v=rs142807316;vdb=variation;vf=28189222


Currently the rest interface for variants seems buggy and incomplete. That may be the wrong impression, but i could find no clue in the documentation that would explain  the current behaviour.


Thank you for your help!


Beat Wolf


________________________________
From: Dev <dev-bounces at ensembl.org> on behalf of Wolf Beat <Beat.Wolf at hefr.ch>
Sent: Saturday, September 2, 2017 11:14:34 AM
To: Ensembl developers list
Subject: [ensembl-dev] REST service

Hello,


i'm trying to extract maf numbers from the REST interface about specific variants.

I'm having trouble parsing the information, because the returned results are not very consistent.


Usually what i'm looking for is one of the following 3 fields in the VEP access point (http://rest.ensembl.org/vep/hsapiens/id)


under colocated_variants there are 3 fields i know of that can have a maf:

minor_allele_freq

exac_maf

gnomad_maf


But not all variants have all of them, or even any of them. For example :

http://rest.ensembl.org/vep/hsapiens/id/rs78935905?ExAC=1&distance=0&content-type=application/json


Lists multiple maf values, but only of subpopulations, none of the overall population. It is also missing the 1000 genomes maf listed on the webiste:

http://grch37.ensembl.org/Homo_sapiens/Variation/Explore?r=2:127820953-127821953;v=rs78935905;vdb=variation;vf=17905322


So, in short, i think there are issues when reporting maf values through the rest interface. Sometimes the informations is missing completely, or is only partially here (like in my example).


Also, is there a list of possible fields? Right now its hard to write a parser, as the returned values can be very different depending on the variant.


By the way, if there is a better way to retrieve the MAF values, then that would be great.


Kind regards


Beat Wolf


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