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Dear Daniel,<br>
<br>
Looking at this region in GRCh37, you can see there is a patch fix
overlapping.<br>
<a class="moz-txt-link-freetext" 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<br>
<br>
<div class="moz-cite-prefix">On 16/06/2017 13:16, Daniel Suveges
wrote:<br>
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<p class="MsoNormal"><span style="font-size:11.0pt" lang="EN-US">Hi
Guys,<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt" lang="EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt" lang="EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt" lang="EN-US">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:<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt" lang="EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt" lang="EN-US">Let’s
take the variant rs11553699 for example:
<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt" lang="EN-US">it’s
GRCh37 coordinates:
</span><span style="font-size:11.0pt">12:122216910<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt" lang="EN-US">it’s
GRCh38 coordinates:
</span><span style="font-size:11.0pt">12:121779004<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt" lang="EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt" lang="EN-US">If
I want to map it’s GRCh37 coordinates to the newer build it
works:<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt" lang="EN-US"><a
href="http://rest.ensembl.org/map/human/GRCh37/12:122216910..122216910:1/GRCh38?content-type=application/json"
moz-do-not-send="true">http://rest.ensembl.org/map/human/GRCh37/12:122216910..122216910:1/GRCh38?content-type=application/json</a><o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt" lang="EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt" lang="EN-US">But
when I’m trying to do the same in the opposite direction,
the ‘mappings’ array is empty in the returned json:<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt" lang="EN-US"><a
href="http://rest.ensembl.org/map/human/GRCh38/12:121779004..121779004:1/GRCh37?content-type=application/json"
moz-do-not-send="true">http://rest.ensembl.org/map/human/GRCh38/12:121779004..121779004:1/GRCh37?content-type=application/json</a><o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt" lang="EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt" lang="EN-US">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.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt" lang="EN-US">Thank
you very much for your help!<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt" lang="EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt" lang="EN-US">Best,<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt" lang="EN-US">Daniel<o:p></o:p></span></p>
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