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

[Cyriac Kandoth]

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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