[ensembl-dev] REST - map endpoint

[Daniel Suveges]

Hi Magali,

Thank you very much for your answer! For me it seems that the patch (HG1595_PATCH 12:121,761,801-122,096,722) is close but does not overlap with this position: 12:122216910. But I might get it wrong, in which case I don’t know why this ambiguity is not listed in the variant annotation:
http://grch37.rest.ensembl.org/variation/human/rs11553699.json
And does not explain why sometimes I have a proper response. Mysterious.

Best,
Daniel

From: Dev <dev-bounces at ensembl.org> on behalf of mag <mr6 at ebi.ac.uk>
Reply-To: Ensembl developers list <dev at ensembl.org>
Date: Friday, 16 June 2017 at 13:44
To: "dev at ensembl.org" <dev at ensembl.org>
Subject: Re: [ensembl-dev] REST - map endpoint

Dear Daniel,

Looking at this region in GRCh37, you can see there is a patch fix overlapping.
http://grch37.ensembl.org/Homo_sapiens/Location/View?r=12:122216910-122216910;db=core

This means that, when attempting to map the region in GRCh38 back to GRCh37, there are two possible results, the region on chromosome 12 and the region in the patch. As the API will only return unambiguous mappings, the query comes back empty.


Hope that helps,
Magali
On 16/06/2017 13:16, Daniel Suveges wrote:
Hi Guys,


I’m trying to use the map endpoint of the REST service (to map between the human GRCh37 and 38 build) and I’m encountering some unexpected behavior:

Let’s take the variant rs11553699 for example:
it’s GRCh37 coordinates: 12:122216910
it’s GRCh38 coordinates: 12:121779004

If I want to map it’s GRCh37 coordinates to the newer build it works:
http://rest.ensembl.org/map/human/GRCh37/12:122216910..122216910:1/GRCh38?content-type=application/json

But when I’m trying to do the same in the opposite direction, the ‘mappings’ array is empty in the returned json:
http://rest.ensembl.org/map/human/GRCh38/12:121779004..121779004:1/GRCh37?content-type=application/json

For other GRCh38 coordinates mapping works, this position has coordinates in both build, so it is not clear to me why the second query seemingly fails.
Thank you very much for your help!

Best,
Daniel




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