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

[Ullman-Cullere, Mollie]

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



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<mailto: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<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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