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<div class="">Hi Daniel,</div>
<div class=""><br class="">
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<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>
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<div class="">Besides, one of the results from Ensembl VEP (with input c.783_661+1del124) is again:</div>
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<div class="">ENST00000460680.1:c.<b class="">661_783+1</b>delGAGCCCTACCACGACATCCGCTTCAACCTGATGGCAGTGGTGCCCGACCGCAGGATCAAGTATGAGGCCAGGCTGCATGTGCTGAAGGTGAACCGTCAGACAGTACTAGAGGCTCTGCAGCAGG</div>
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<div class="">As far as I know, VEP returns HGVS compliant syntax. So, should it not also accept the same as input?</div>
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<div class="">Cheers,</div>
<div class="">Bhavana</div>
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<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 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: <dev-bounces@ensembl.org<mailto:dev-bounces@ensembl.org>> on behalf of Bhavana Harsha <bh4@sanger.ac.uk<mailto:bh4@sanger.ac.uk>><br class="">
Reply-To: Ensembl developers list <dev@ensembl.org<mailto:dev@ensembl.org>><br class="">
Date: Friday, September 16, 2016 at 3:40 PM<br class="">
To: "dev@ensembl.org<mailto:dev@ensembl.org>" <dev@ensembl.org<mailto:dev@ensembl.org>><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="">
http://grch37.rest.ensembl.org/vep/human/hgvs/ENST00000460680.1:c.661_783+1del124?content-type=application/json;canonical=1&ccds=1&hgvs=1<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="">
http://grch37.rest.ensembl.org/vep/human/hgvs/ENST00000460680.1:c.661_783+1delGAGCCCTACCACGACATCCGCTTCAACCTGATGGCAGTGGTGCCCGACCGCAGGATCAAGTATGAGGCCAGGCTGCATGTGCTGAAGGTGAACCGTCAGACAGTACTAGAGGCTCTGCAGCAGG?content-type=application/json;canonical=1&ccds=1&hgvs=1<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="">
</blockquote>
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