[ensembl-dev] VEP on GRCh37 variants, using Gencode v24 transcripts

[Will McLaren]

Hi Cyriac,

Your current strategy is currently the best one. There are no concrete
plans as I write to import the backmapped GENCODE files to an Ensembl
database that would then be used to generate a VEP cache.

Regards

Will McLaren
Ensembl Variation

On 15 July 2016 at 20:16, Cyriac Kandoth <kandothc at mskcc.org> wrote:

> Hi VEP team,
>
> From what I understand, online/offline VEP v84 uses transcripts from
> Ensembl v75 (Gencode v19), when the input variants are GRCh37. What is the
> least resistance way to take advantage of Gencode v24 transcripts, in a
> variant annotation pipeline that has to report calls in GRCh37.
>
> My current strategy creates a custom VEP cache based on the liftOvered
> GFFs that Gencode provides (
> http://www.gencodegenes.org/releases/24lift37.html), but I miss all the
> supplemental annotations that the official caches contain.
>
> ~Cyriac
>
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