[ensembl-dev] REST - map endpoint

[mag]

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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