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

[Cyriac Kandoth]

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> 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
>
>
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