[ensembl-dev] VEP reporting HGVS format for an insertion without 3' shifting across tandem repeat

Sarah Hunt seh at ebi.ac.uk
Fri May 22 16:51:53 BST 2015


Hi Cyriac,

The --shift_hgvs option is available in v79, so do try it and let us 
know if the results are not what you expect.

All the best,

Sarah

On 22/05/2015 16:46, Cyriac Kandoth wrote:
> Thanks very much Sarah. This is good to know. We're using VEP v79 in 
> offline more, on command line, on GRCh37 loci. Do we need to update to 
> v80, to be able to use the --shift-hgvs option?
>
> Cheers!
>
> ~Cyriac
>
> On Fri, May 22, 2015 at 4:39 AM, Sarah Hunt <seh at ebi.ac.uk 
> <mailto:seh at ebi.ac.uk>> wrote:
>
>
>     Hi Cyriac,
>
>     Thanks for the query - could you supply a bit more information?.
>     Are you using VEP through the web site, REST or by command line?
>     Is your data on GRCh37 or GRCh38?
>
>     Prior to e!80, non-shifted desriptions were our default and the
>     --shift_hgvs option had to be selected when using the command line
>     script to produce 3' shifted HGVS annotation. As of e!80, shifted
>     descriptions will be the default and there will be a command line
>     option to turn them off.
>
>     The GRCh38 website was updated to e!80 yesterday and the GRCh37
>     site will be updated shortly.
>
>     Best wishes,
>
>     Sarah
>
>
>     On 21/05/2015 20:29, Cyriac Kandoth wrote:
>>     Here is a VCF-format example of an insertion within a tandem
>>     repeat region, that reports HGVSp = p.Ala771_Tyr772ins.
>>     17 37880984 . A ATACGTGATGGCT . . .
>>
>>     HGVS, at least for deletions, states "the most 3' position
>>     possible is arbitrarily assigned to have been changed". This is
>>     different from the oft-used convention of "left-shifting" indels.
>>     So what's the correct solution here?
>>
>>     This one's pretty complicated and I'm still trying to get my head
>>     around it. But I would love to hear from someone who worked on
>>     implementing HGVS notations into VEP.
>>
>>     Thanks!
>>
>>     ~Cyriac
>>
>>
>>     _______________________________________________
>>     Dev mailing listDev at ensembl.org  <mailto:Dev at ensembl.org>
>>     Posting guidelines and subscribe/unsubscribe info:http://lists.ensembl.org/mailman/listinfo/dev
>>     Ensembl Blog:http://www.ensembl.info/
>
>
>     _______________________________________________
>     Dev mailing list Dev at ensembl.org <mailto:Dev at ensembl.org>
>     Posting guidelines and subscribe/unsubscribe info:
>     http://lists.ensembl.org/mailman/listinfo/dev
>     Ensembl Blog: http://www.ensembl.info/
>
>
>
>
> _______________________________________________
> 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/20150522/0ea5b2ff/attachment.html>


More information about the Dev mailing list