[ensembl-dev] REST service

[Wolf Beat]

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