[ensembl-dev] Missing MAF numbers on VEP REST service
Wolf Beat
Beat.Wolf at hefr.ch
Sun Jul 31 08:39:55 BST 2016
Hello,
i recently migrated a lot of my code from the biomart interface to the ensembl rest service. I'm mainly using grch37 as my source.
I made the following observation:
When i query a multi allelic variant, the REST VEP service returns not MAF numbers.
But when i query the biomart service or check the variant on the website manually, the MAF numbers are present.
Just to give one example:
Variant rs6687605 has an MAF number of 0.43 when looked at on the website and biomart:
http://grch37.ensembl.org/Homo_sapiens/Variation/Explore?r=1:25889132-25890132;v=rs6687605;vdb=variation;vf=106422589
But the REST service returns no MAF number:
http://grch37.rest.ensembl.org/vep/hsapiens/id/rs6687605?content-type=application/json
I observed the same behaviour for:
rs2229546, rs6022, rs1058111
I also observed that the VEP rest service specifies:
http://grch37.rest.ensembl.org/documentation/info/vep_id_get
That the ExAC information is by default off. But i do recieve it without specifying the option.
In my case i actually want it, but its still interesting to note.
The first problem is kind of a big issue for me, any help in solving it would be greatly appreciated.
Kind regards
Beat Wolf
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