[ensembl-dev] VEP e!90 HGVS del/dup bases removed?
Sarah Hunt
seh at ebi.ac.uk
Mon Dec 11 13:44:00 GMT 2017
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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