[ensembl-dev] VEP result does not match start-end coordinate and allele for hgvs syntax

Bhavana Harsha bh4 at sanger.ac.uk
Thu Sep 22 10:32:00 BST 2016


Hi Sarah,

Thank you for fixing this. I updated my code and it runs successfully now.

Cheers,
Bhavana

On 20 Sep 2016, at 11:16, dev-request at ensembl.org<mailto:dev-request at ensembl.org> wrote:

Message: 1
Date: Mon, 19 Sep 2016 14:31:01 +0100
From: Sarah Hunt <seh at ebi.ac.uk<mailto:seh at ebi.ac.uk>>
Subject: Re: [ensembl-dev] VEP result does not match start-end
coordinate and allele for hgvs syntax
To: dev at ensembl.org<mailto:dev at ensembl.org>
Message-ID: <1cdd0a5c-bd3e-5acf-ffa4-0e3847a80cd8 at ebi.ac.uk<mailto:1cdd0a5c-bd3e-5acf-ffa4-0e3847a80cd8 at ebi.ac.uk>>
Content-Type: text/plain; charset="windows-1252"; Format="flowed"


Hi Bhavana,

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.

Best wishes,

Sarah


On 19/09/2016 10:34, Bhavana Harsha wrote:
Hi Daniel,

Thank you for this. It works on VEP REST when I reverse the coordinates.
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?).

Besides, one of the results from Ensembl VEP (with input
c.783_661+1del124) is again:

ENST00000460680.1:c.*661_783+1*delGAGCCCTACCACGACATCCGCTTCAACCTGATGGCAGTGGTGCCCGACCGCAGGATCAAGTATGAGGCCAGGCTGCATGTGCTGAAGGTGAACCGTCAGACAGTACTAGAGGCTCTGCAGCAGG

As far as I know, VEP returns HGVS compliant syntax. So, should it not
also accept the same as input?

Cheers,
Bhavana


HI Bhavana,

I think the transcript is on the -1 strand so the start/end
coordinates have to be swapped.
http://grch37.rest.ensembl.org/vep/human/hgvs/ENST00000460680.1:c.783_661+1del124?content-type=application/json;canonical=1&ccds=1&hgvs=1

But that's just a guess.
Best,
Daniel

From: <dev-bounces at ensembl.org<mailto:dev-bounces at ensembl.org><mailto:dev-bounces at ensembl.org>> on
behalf of Bhavana Harsha <bh4 at sanger.ac.uk<mailto:bh4 at sanger.ac.uk><mailto:bh4 at sanger.ac.uk>>
Reply-To: Ensembl developers list
<dev at ensembl.org<mailto:dev at ensembl.org><mailto:dev at ensembl.org>>
Date: Friday, September 16, 2016 at 3:40 PM
To: "dev at ensembl.org<mailto:dev at ensembl.org><mailto:dev at ensembl.org>"
<dev at ensembl.org<mailto:dev at ensembl.org><mailto:dev at ensembl.org>>
Subject: [ensembl-dev] VEP result does not match start-end
coordinate and allele for hgvs syntax

Hello,

We?re trying to validate some mutations and see other co-located
variants by using the VEP REST service for GRCh37, like this:

http://grch37.rest.ensembl.org/vep/human/hgvs/ENST00000460680.1:c.661_783+1del124?content-type=application/json;canonical=1&ccds=1&hgvs=1

And I get the following error:
{?error":"Start (52440390) must be less than or equal to end+1
(52440270)"}


If I include the deleted sequence in the hgvs syntax, I get a
different error:

Input:
http://grch37.rest.ensembl.org/vep/human/hgvs/ENST00000460680.1:c.661_783+1delGAGCCCTACCACGACATCCGCTTCAACCTGATGGCAGTGGTGCCCGACCGCAGGATCAAGTATGAGGCCAGGCTGCATGTGCTGAAGGTGAACCGTCAGACAGTACTAGAGGCTCTGCAGCAGG?content-type=application/json;canonical=1&ccds=1&hgvs=1

Output:
{?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)"}


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.

Is there something I?m missing here?

Cheers,
Bhavana


---------------------------------------------
Bhavana Harsha
Bioinformatician
COSMIC
Wellcome Trust Sanger Institute
Hinxton, UK
CB10 1SA


-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mail.ensembl.org/pipermail/dev_ensembl.org/attachments/20160922/d4392a88/attachment.html>


More information about the Dev mailing list