[ensembl-dev] REST API - overlap endpoint with variant_set option

[Daniel Suveges]

Hi Sarah,


Thank you very much for the quick reply and for fixing this issue!

Best,
Daniel

From: <dev-bounces at ensembl.org<mailto:dev-bounces at ensembl.org>> on behalf of Sarah Hunt <seh at ebi.ac.uk<mailto:seh at ebi.ac.uk>>
Reply-To: Ensembl developers list <dev at ensembl.org<mailto:dev at ensembl.org>>
Date: Tuesday, January 24, 2017 at 1:41 PM
To: "dev at ensembl.org<mailto:dev at ensembl.org>" <dev at ensembl.org<mailto:dev at ensembl.org>>
Subject: Re: [ensembl-dev] REST API - overlap endpoint with variant_set option



Hi Daniel,

Thanks for reporting this one. There is a data problem in the GRCh37 database and GWAS catalog variants are not associated with the 'NHGRI-EBI GWAS catalog' or 'ph_variants' set. Until we can fix the data in our March release, this would have to be a two step process, extracting all variants by region then looking up by id to filter the for those with phenotype information.

Best wishes,

Sarah

On 24/01/2017 12:39, Daniel Suveges wrote:
Hi Guys,


I'm planning to use the overlap endpoint of the REST API to get a list of variants which have phenotype annotations using the 'variant_set=ph_variants' option. However it does not work as I expected. Let's take a GWAS hit rs1314913, a variant with phenotype annotation:

wget -q --header='Content-type:application/json' --header='Accept:application/json' --post-data='{ "ids" : ["rs1314913" ] }' 'http://grch37.rest.ensembl.org/variation/homo_sapiens?phenotypes=1'  -O -

The output looks alright, the variant has the expected phenotype annotation. But when querying the same region, the variant is not listed:

wget -q 'http://grch37.rest.ensembl.org/overlap/region/human/14:68699592-68699596?feature=variation;content-type=application/json;variant_set=ph_variants' -O -

If the variant_set option is removed, the variant is there:

wget -q 'http://grch37.rest.ensembl.org/overlap/region/human/14:68699592-68699596?feature=variation;content-type=application/json' -O -

This example works well on the newer genome build, so this issue is probably GRCh37 specific.
Thanks for your help!

Best,
Daniel






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