[ensembl-dev] RegulatoryFeatures in VEP v79?

Konrad Karczewski konradk at broadinstitute.org
Thu May 21 13:56:41 BST 2015

Hi Daniel,

Ah ok great thanks! Thing is though: now none of the 10M variants in ExAC overlap RegulatoryFeatures. Is that expected? I would have expected at least a few...


On Thu, May 21, 2015 at 2:17 AM, Daniel Zerbino <zerbino at ebi.ac.uk> wrote:

> Hello Konrad,
> this is because on release 79 we replaced the old regulatory build with 
> the newer version (which we had released for GRCh38 in v76).
> There would definitely be some moving around of features as both builds 
> are very different in the way they are computed.
> Regards,
> Daniel
> On 5/21/15 5:28 AM, Konrad Karczewski wrote:
>> Hi Will, everyone,
>> Are RegulatoryFeature annotations expected to have the same results in 
>> VEP v79 (GRCh37) as previous versions (e.g. v77)? When annotating the 
>> ExAC VCF, the older versions included many ENSR* annotations, but 
>> v79's do not (same command including --everything both times). For 
>> instance, the following variant used to overlap ENSR00000528767 but 
>> does not seem to in my most recent version:
>> 1       13372   .       G       C
>> Any idea why this might be happening? All other annotations seem fine.
>> Thanks!
>> -Konrad
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