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

[Sarah Hunt]

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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