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<p>Hi Bhavana,</p>
<p>Thanks for reporting this one - you have discovered a bug in our
HGVS parsing of longer variants. This is now fixed in the
release/85 variation API, so if you use command line VEP, you
could pick up the update. We are in the late stages of preparing
for our next release which is due at the end of the month, so our
REST and web servers will be updated then.</p>
<p>Best wishes,</p>
<p>Sarah<br>
</p>
<br>
<div class="moz-cite-prefix">On 19/09/2016 10:34, Bhavana Harsha
wrote:<br>
</div>
<blockquote
cite="mid:20160919093426.5F5DB22DE0F_7DFB122B@hx-mx1.ebi.ac.uk"
type="cite">
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<div class="">Hi Daniel,</div>
<div class=""><br class="">
</div>
<div class="">Thank you for this. It works on VEP REST when I
reverse the coordinates.</div>
<div class="">But from what I know reversing the coordinates is
not compliant with the HGVS notation rules (i.e. the positions
should be listed 5’ to 3’).</div>
<div class=""><br class="">
</div>
<div class="">Besides, one of the results from Ensembl VEP (with
input c.783_661+1del124) is again:</div>
<div class=""><br class="">
</div>
<div class="">ENST00000460680.1:c.<b class="">661_783+1</b>delGAGCCCTACCACGACATCCGCTTCAACCTGATGGCAGTGGTGCCCGACCGCAGGATCAAGTATGAGGCCAGGCTGCATGTGCTGAAGGTGAACCGTCAGACAGTACTAGAGGCTCTGCAGCAGG</div>
<div class=""><br class="">
</div>
<div class="">As far as I know, VEP returns HGVS compliant syntax.
So, should it not also accept the same as input?</div>
<div class=""><br class="">
</div>
<div class="">Cheers,</div>
<div class="">Bhavana</div>
<div class=""><br class="">
</div>
<br class="">
<blockquote type="cite" class="">HI Bhavana,<br class="">
<br class="">
I think the transcript is on the -1 strand so the start/end
coordinates have to be swapped.<br class="">
<a moz-do-not-send="true"
href="http://grch37.rest.ensembl.org/vep/human/hgvs/ENST00000460680.1:c.783_661+1del124?content-type=application/json;canonical=1&ccds=1&hgvs=1"
class="">http://grch37.rest.ensembl.org/vep/human/hgvs/ENST00000460680.1:c.783_661+1del124?content-type=application/json;canonical=1&ccds=1&hgvs=1</a><br
class="">
<br class="">
But that's just a guess.<br class="">
Best,<br class="">
Daniel<br class="">
<br class="">
<blockquote type="cite" class="">From:
<<a class="moz-txt-link-abbreviated" href="mailto:dev-bounces@ensembl.org">dev-bounces@ensembl.org</a><a class="moz-txt-link-rfc2396E" href="mailto:dev-bounces@ensembl.org"><mailto:dev-bounces@ensembl.org></a>>
on behalf of Bhavana Harsha
<<a class="moz-txt-link-abbreviated" href="mailto:bh4@sanger.ac.uk">bh4@sanger.ac.uk</a><a class="moz-txt-link-rfc2396E" href="mailto:bh4@sanger.ac.uk"><mailto:bh4@sanger.ac.uk></a>><br
class="">
Reply-To: Ensembl developers list
<<a class="moz-txt-link-abbreviated" href="mailto:dev@ensembl.org">dev@ensembl.org</a><a class="moz-txt-link-rfc2396E" href="mailto:dev@ensembl.org"><mailto:dev@ensembl.org></a>><br
class="">
Date: Friday, September 16, 2016 at 3:40 PM<br class="">
To: "<a class="moz-txt-link-abbreviated" href="mailto:dev@ensembl.org">dev@ensembl.org</a><a class="moz-txt-link-rfc2396E" href="mailto:dev@ensembl.org"><mailto:dev@ensembl.org></a>"
<<a class="moz-txt-link-abbreviated" href="mailto:dev@ensembl.org">dev@ensembl.org</a><a class="moz-txt-link-rfc2396E" href="mailto:dev@ensembl.org"><mailto:dev@ensembl.org></a>><br
class="">
Subject: [ensembl-dev] VEP result does not match start-end
coordinate and allele for hgvs syntax<br class="">
<br class="">
Hello,<br class="">
<br class="">
We?re trying to validate some mutations and see other
co-located variants by using the VEP REST service for GRCh37,
like this:<br class="">
<br class="">
<a class="moz-txt-link-freetext" href="http://grch37.rest.ensembl.org/vep/human/hgvs/ENST00000460680.1:c.661_783+1del124?content-type=application/json;canonical=1&ccds=1&hgvs=1">http://grch37.rest.ensembl.org/vep/human/hgvs/ENST00000460680.1:c.661_783+1del124?content-type=application/json;canonical=1&ccds=1&hgvs=1</a><br
class="">
<br class="">
And I get the following error:<br class="">
{?error":"Start (52440390) must be less than or equal to end+1
(52440270)"}<br class="">
<br class="">
<br class="">
If I include the deleted sequence in the hgvs syntax, I get a
different error:<br class="">
<br class="">
Input:<br class="">
<a class="moz-txt-link-freetext" href="http://grch37.rest.ensembl.org/vep/human/hgvs/ENST00000460680.1:c.661_783+1delGAGCCCTACCACGACATCCGCTTCAACCTGATGGCAGTGGTGCCCGACCGCAGGATCAAGTATGAGGCCAGGCTGCATGTGCTGAAGGTGAACCGTCAGACAGTACTAGAGGCTCTGCAGCAGG?content-type=application/json;canonical=1&ccds=1&hgvs=1">http://grch37.rest.ensembl.org/vep/human/hgvs/ENST00000460680.1:c.661_783+1delGAGCCCTACCACGACATCCGCTTCAACCTGATGGCAGTGGTGCCCGACCGCAGGATCAAGTATGAGGCCAGGCTGCATGTGCTGAAGGTGAACCGTCAGACAGTACTAGAGGCTCTGCAGCAGG?content-type=application/json;canonical=1&ccds=1&hgvs=1</a><br
class="">
<br class="">
Output:<br class="">
{?error":"Reference allele extracted from
ENST00000460680:52440390-52440269 (AGCCCTACCACGACATCCGCTTCAACCTGATGGCAGTGGTGCCCGACCGCAGGATCAAGTATGAGGCCAGGCTGCATGTGCTGAAGGTGAACCGTCAGACAGTACTAGAGGCTCTGCAGCAG)
does not match reference allele given by HGVS
notation ENST00000460680.1:c.661_783+1delGAGCCCTACCACGACATCCGCTTCAACCTGATGGCAGTGGTGCCCGACCGCAGGATCAAGTATGAGGCCAGGCTGCATGTGCTGAAGGTGAACCGTCAGACAGTACTAGAGGCTCTGCAGCAGG
(GAGCCCTACCACGACATCCGCTTCAACCTGATGGCAGTGGTGCCCGACCGCAGGATCAAGTATGAGGCCAGGCTGCATGTGCTGAAGGTGAACCGTCAGACAGTACTAGAGGCTCTGCAGCAGG)"}<br
class="">
<br class="">
<br class="">
This is strange because shouldn?t the transcript coordinates
?ENST00000460680.1:c.661-783+1? correspond to
?3:g.52440268-52440391?? But these aren?t the coordinates
returned and the allele sequence is inconsistent with the
input.<br class="">
<br class="">
Is there something I?m missing here?<br class="">
<br class="">
Cheers,<br class="">
Bhavana<br class="">
<br class="">
<br class="">
---------------------------------------------<br class="">
Bhavana Harsha<br class="">
Bioinformatician<br class="">
COSMIC<br class="">
Wellcome Trust Sanger Institute<br class="">
Hinxton, UK<br class="">
CB10 1SA<br class="">
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