[ensembl-dev] plants.ensembl.org questions

[Olson, Andrew]

Sample genotypes are accessed by the web server to a remotely hosted index vcf file instead of in the ensembl variation database. The MAF for a variant obtained from this remote file. As far as I know, the biomart database build does not gather sample alleles from these remotely hosted vcf files. However, one way to get it programmatically is from the EVA rest API:
https://www.ebi.ac.uk/eva/webservices/rest/swagger-ui.html
It didn’t work for me given the variant ID ENSVATH02373908, but id did work with a segments query
https://www.ebi.ac.uk/eva/webservices/rest/v1/segments/3%3A15142729-15142729/variants?species=athaliana_tair10

Andrew

On Oct 9, 2017, at 10:10 AM, Wolf Beat <Beat.Wolf at hefr.ch<mailto:Beat.Wolf at hefr.ch>> wrote:

Hello,


i have 2 questions about plants.ensembl.org<http://plants.ensembl.org>


First, is there a rest interface similar to the main ensembl release?


Second, is there a way to find the minor allele frequence through the biomart interface?


For example this variant:

https://urldefense.proofpoint.com/v2/url?u=http-3A__plants.ensembl.org_Arabidopsis-5Fthaliana_Variation_Explore-3Fr-3D3-3A15142229-2D15143229-3Bv-3DENSVATH02373908-3Bvdb-3Dvariation-3Bvf-3D7087020&d=DwICAg&c=mkpgQs82XaCKIwNV8b32dmVOmERqJe4bBOtF0CetP9Y&r=ic-pQ08gnhTpvpqfp3_6Uw&m=Sk5LhgZF6Gtx39HDqDIDUmZyOA2hs0elnvr8Vbrx0Lw&s=kOstIMPNzVgL6yRgjn5wk0lG6cc27m0-DvJpJJ_o_aY&e=


States that the MAF is < 0.01. Yet the biomart interface returns nothing when retrieving the minor_allele_freq for this variant. Is there a different way to get it?


Kind regards


Beat Wolf
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