[ensembl-dev] VEP e!90 HGVS del/dup bases removed?
Sarah Hunt
seh at ebi.ac.uk
Mon Dec 11 15:35:00 GMT 2017
Hi Luke,
Thanks for this suggestion - we will add this functionality.
All the best,
Sarah
On 11/12/2017 15:17, Luke Goodsell wrote:
>
> Hi Sarah,
>
> Indeed, that would be very helpful.
>
> Kind regards,
>
> Luke
>
> *From: *Dev <dev-bounces at ensembl.org> on behalf of Sarah Hunt
> <seh at ebi.ac.uk>
> *Reply-To: *Ensembl developers list <dev at ensembl.org>
> *Date: *Monday, 11 December 2017 at 15:16
> *To: *Ensembl developers list <dev at ensembl.org>
> *Subject: *Re: [ensembl-dev] VEP e!90 HGVS del/dup bases removed?
>
>
> Hi Luke,
>
> We don't have a thread to share for this one. If the deleted reference
> allele used was reported seperately, would this be adequate for your
> checks?
>
> Sarah
>
> On 11/12/2017 14:01, Luke Goodsell wrote:
>
> Hi Sarah,
>
> Thanks for providing an answer so quickly.
>
> Is there a thread I can read through where this change was
> discussed? I’d like to better understand the rationale for
> discarding the bases rather than having them, say, optionally
> removed. Just because they aren’t canonical or perfect in all
> situations doesn’t mean they aren’t useful in some situations.
>
> Kind regards,
>
> Luke
>
> *From: *Dev <dev-bounces at ensembl.org>
> <mailto:dev-bounces at ensembl.org> on behalf of Sarah Hunt
> <seh at ebi.ac.uk> <mailto:seh at ebi.ac.uk>
> *Reply-To: *Ensembl developers list <dev at ensembl.org>
> <mailto:dev at ensembl.org>
> *Date: *Monday, 11 December 2017 at 13:44
> *To: *Ensembl developers list <dev at ensembl.org>
> <mailto:dev at ensembl.org>
> *Subject: *Re: [ensembl-dev] VEP e!90 HGVS del/dup bases removed?
>
> Hi Luke,
>
> After discussions with collaborators on the myriad of different
> ways the same allele can be represented in HGVS, we removed the
> deleted/duplicated bases to conform with the recommended rather
> than permitted version of the nomenclature. There isn't a way to
> include them at the moment. This could be added, but it would
> contribute to the difficulty in comparing annotations across
> different sources.
>
> Best wishes,
>
> Sarah
>
> On 11/12/2017 13:18, Luke Goodsell wrote:
>
> Hi,
>
> We’ve noticed since upgrading from e!88 to e!90 that the
> deleted/duplicated bases are no longer being reported in HGVS
> strings. Is there a way to include them?
>
> Out of curiosity, why were they removed? It was my
> understanding that they are not required by the HGVS spec, but
> that they can be optionally included. We use them downstream
> as a way to double-check the variant annotation.
>
> Kind regards,
>
> Luke
>
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