[ensembl-dev] VEP - HGVS syntax coords reversed

[Bhavana Harsha]

Hello Sarah,

Thank you for getting back.
I’ll pull the changes to my local checkout.

Cheers,
Bhavana

> Date: Mon, 24 Jul 2017 17:18:37 +0100
> From: Sarah Hunt <seh at ebi.ac.uk>
> To: dev at ensembl.org
> Subject: Re: [ensembl-dev] VEP - HGVS syntax coords reversed
> Message-ID: <8d034773-d001-63f6-c397-7dda55f63dca at ebi.ac.uk>
> Content-Type: text/plain; charset="windows-1252"; Format="flowed"
> 
> 
> Hi Bhavana,
> 
> Thanks for reporting this one. It will be fixed when we update our REST 
> servers for our new release next month. If you are running VEP on the 
> command line, you can pick up the fix by updating your copy of the 
> ensembl-variation API.
> 
> Sorry for the delay in getting back to you - do let us know if you spot 
> any other odd cases.
> 
> Best wishes,
> 
> Sarah
> 
> On 10/07/2017 16:23, Bhavana Harsha wrote:
>> Hello,
>> 
>> I?m trying to look at the transcript consequences of the following 
>> variant:
>> 17:g.7577607_7578174del
>> 
>> using the REST API like this:
>> http://grch37.rest.ensembl.org/vep/human/hgvs/17:g.7577607_7578174del?content-type=application/json;xref_refseq=1&canonical=1&ccds=1&hgvs=1
>> 
>> This is what I get for one of the transcripts:
>> ENST00000269305.4:c.674_672+3delCTGG?.
>> 
>> Shouldn?t the correct syntax be ENST00000269305.4:c.*672+3_674*delCTGG..?
>> 
>> (Other transcript consequences for this variant appear to have a 
>> similar issue - ENST00000504290.1:n.556_554+3delCTGGT?)
>> 
>> I get the same result using the VEP web interface.
>> 
>> 
>> 
>> Regards,
>> Bhavana
>> 
>> 
>> 
>> 
>> 
>> 
>> ---------------------------------------------
>> Bhavana Harsha
>> Bioinformatician
>> COSMIC
>> Wellcome Trust Sanger Institute
>> Hinxton, UK
>> CB10 1SA