[ensembl-dev] VEP reporting HGVS format for an insertion without 3' shifting across tandem repeat
seh at ebi.ac.uk
Fri May 22 09:39:51 BST 2015
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.
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.
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