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

Mon Dec 11 15:17:57 GMT 2017

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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