[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
>>
>>
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