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

[Will McLaren]

Hello

Shifting HGVS became the default in release 80. You may disable it with
"--shift_hgvs 0".

In release 79 (and 77, 78 and 79), you had to enable it with "--shift_hgvs".

Regards

Will McLaren
Ensembl Variation

On 8 July 2015 at 15:51, Ullman-Cullere, Mollie <MULLMANCULLERE at partners.org
> wrote:

>  Question:
>
> If --shift_hgvs works in VEPv79, is it on by default, as it is with
> VEPv80?
>
> We’re running v79 without this flag and want to confirm that we’ll not see
> the shift.
>
>
>
> Thanks in advance,
>
> Mollie
>
>
>
>
>
>
>
> *Mollie Ullman-Cullere Sr. Clinical Bioinformaticist Clinical and
> Translational Informatics Dana-Farber Cancer Institute/Partners Healthcare
> Cell: 617-817-1496 <617-817-1496>*
>
>
>
>
>
>
>
> *From:* dev-bounces at ensembl.org [mailto:dev-bounces at ensembl.org] *On
> Behalf Of *Cyriac Kandoth
> *Sent:* Friday, May 22, 2015 3:21 PM
> *To:* Ensembl developers list
> *Cc:* Ahmet Zehir; Nikolaus D. Schultz; Wang, Qingguo/Sloan Kettering
> Institute
> *Subject:* Re: [ensembl-dev] VEP reporting HGVS format for an insertion
> without 3' shifting across tandem repeat
>
>
>
> 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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