[ensembl-dev] VEP : Incorrect hgvsp syntax

[Sarah Hunt]

Hi Bhavana,

Thanks for the clarification. This is an interesting example - the long 
deletion spanning 2 exons and a full intron is not being handled 
correctly. It won't be possible to update our REST or web tools until 
our next release, but we will let you know when the code is updated.

Best wishes,

Sarah


On 26/09/2017 10:16, Bhavana Harsha wrote:
> Hello,
>
> I seem to have mixed two separate examples in my email, sorry.
> These are the correct ones:
>
> Input : 3:g.41266031_41266626del
> http://grch37.rest.ensembl.org/vep/human/hgvs/3:g.41266031_41266626del?content-type=application/json;xref_refseq=1&canonical=1&ccds=1&hgvs=1 
> <http://grch37.rest.ensembl.org/vep/human/hgvs/3:g.41266017_41266633del?content-type=application/json;xref_refseq=1&canonical=1&ccds=1&hgvs=1>
> VEP returns : ENSP00000344456.5:p.Leu10_Ter142delinsTyr
> Correct result : ENSP00000344456.5:p.Leu10_Asn141del
>
> Cheers,
> Bhavana
>
>
>> On 25 Sep 2017, at 17:01, Bhavana Harsha <bh4 at sanger.ac.uk 
>> <mailto:bh4 at sanger.ac.uk>> wrote:
>>
>> Hello,
>>
>> When I run VEP (GRCh37) using the following input :
>> 3:g.41266017_41266633del
>>
>> I get ‘ENSP00000379486.3:p.Leu10_Ter142delinsTyr’
>>
>> We think the protein change should be ‘p.Leu10_Asn141del’, as 
>> confirmed by Mutalyzer.
>>
>> The ref peptide sequence returned does not correspond to the protein 
>> sequence in Ensembl for ‘ENSP00000379486.3’. (They start to deviate 
>> at position 80).
>>
>> I ran VEP using the REST API as well as the web interface, for GRCh37.
>> http://grch37.rest.ensembl.org/vep/human/hgvs/3:g.41266031_41266626del?content-type=application/json;xref_refseq=1&canonical=1&ccds=1&hgvs=1
>>
>>
>> Is there something I’m doing wrong?
>>
>>
>> Regards,
>> Bhavana
>>
>>
>>
>>
>> ---------------------------------------------
>> Bhavana Harsha
>> Bioinformatician
>> COSMIC
>> Wellcome Trust Sanger Institute
>> Hinxton, UK
>> CB10 1SA
>>
>>
>>
>
>
>
> _______________________________________________
> Dev mailing list    Dev at ensembl.org
> Posting guidelines and subscribe/unsubscribe info: http://lists.ensembl.org/mailman/listinfo/dev
> Ensembl Blog: http://www.ensembl.info/

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mail.ensembl.org/pipermail/dev_ensembl.org/attachments/20170926/39b38c56/attachment.html>