[ensembl-dev] VEP e!90 HGVS del/dup bases removed?

Sarah Hunt seh at ebi.ac.uk
Mon Dec 11 15:16:30 GMT 2017


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> 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 13:44
> *To: *Ensembl developers list <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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