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<p class="MsoNormal"><span style="font-size:11.0pt">Hi Magali,<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt">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:<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt">http://grch37.rest.ensembl.org/variation/human/rs11553699.json <o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt">And does not explain why sometimes I have a proper response. Mysterious.
<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt">Best,<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt">Daniel<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt"><o:p> </o:p></span></p>
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<p class="MsoNormal"><b><span style="color:black">From: </span></b><span style="color:black">Dev <dev-bounces@ensembl.org> on behalf of mag <mr6@ebi.ac.uk><br>
<b>Reply-To: </b>Ensembl developers list <dev@ensembl.org><br>
<b>Date: </b>Friday, 16 June 2017 at 13:44<br>
<b>To: </b>"dev@ensembl.org" <dev@ensembl.org><br>
<b>Subject: </b>Re: [ensembl-dev] REST - map endpoint</span><span style="color:black;mso-fareast-language:EN-GB"><o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-family:"Times New Roman""><o:p> </o:p></span></p>
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<p class="MsoNormal" style="margin-bottom:12.0pt">Dear Daniel,<br>
<br>
Looking at this region in GRCh37, you can see there is a patch fix overlapping.<br>
<a href="http://grch37.ensembl.org/Homo_sapiens/Location/View?r=12:122216910-122216910;db=core">http://grch37.ensembl.org/Homo_sapiens/Location/View?r=12:122216910-122216910;db=core</a><br>
<br>
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.<br>
<br>
<br>
Hope that helps,<br>
Magali<o:p></o:p></p>
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<p class="MsoNormal">On 16/06/2017 13:16, Daniel Suveges wrote:<o:p></o:p></p>
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<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt">Hi Guys,</span><o:p></o:p></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt"> </span><o:p></o:p></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt"> </span><o:p></o:p></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt">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:</span><o:p></o:p></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt"> </span><o:p></o:p></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt">Let’s take the variant rs11553699 for example:
</span><o:p></o:p></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt">it’s GRCh37 coordinates:
</span><span style="font-size:11.0pt">12:122216910</span><o:p></o:p></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt">it’s GRCh38 coordinates:
</span><span style="font-size:11.0pt">12:121779004</span><o:p></o:p></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt"> </span><o:p></o:p></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt">If I want to map it’s GRCh37 coordinates to the newer build it works:</span><o:p></o:p></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt"><a href="http://rest.ensembl.org/map/human/GRCh37/12:122216910..122216910:1/GRCh38?content-type=application/json">http://rest.ensembl.org/map/human/GRCh37/12:122216910..122216910:1/GRCh38?content-type=application/json</a></span><o:p></o:p></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt"> </span><o:p></o:p></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt">But when I’m trying to do the same in the opposite direction, the ‘mappings’ array is empty in the returned json:</span><o:p></o:p></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt"><a href="http://rest.ensembl.org/map/human/GRCh38/12:121779004..121779004:1/GRCh37?content-type=application/json">http://rest.ensembl.org/map/human/GRCh38/12:121779004..121779004:1/GRCh37?content-type=application/json</a></span><o:p></o:p></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt"> </span><o:p></o:p></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt">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.</span><o:p></o:p></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt">Thank you very much for your help!</span><o:p></o:p></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt"> </span><o:p></o:p></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt">Best,</span><o:p></o:p></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt">Daniel</span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-family:"Times New Roman";mso-fareast-language:EN-GB"><br>
<br>
<br>
<o:p></o:p></span></p>
<pre>_______________________________________________<o:p></o:p></pre>
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<pre>Ensembl Blog: <a href="http://www.ensembl.info/">http://www.ensembl.info/</a><o:p></o:p></pre>
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<br>
<o:p></o:p></span></p>
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