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

[Sarah Hunt]

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
>
>
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