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

Cyriac Kandoth kandoth at cbio.mskcc.org
Fri May 22 20:20:59 BST 2015


Thanks. --shift_hgvs works in VEP v79, but note that it was not listed in
the documentation:
http://mar2015.archive.ensembl.org/info/docs/tools/vep/script/vep_options.html#basic

The annotation for the VCF variant below, changed
from p.Ala771_Tyr772insTyrValMetAla to p.Tyr772_Ala775dup... and we prefer
the latter. Thanks so much!
17 37880984 . A ATACGTGATGGCT . . .

~Cyriac

On Fri, May 22, 2015 at 11:51 AM, Sarah Hunt <seh at ebi.ac.uk> wrote:

>
> 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> 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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>
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