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

[Daniel Suveges]

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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