[ensembl-dev] RegulatoryFeatures in VEP v79?

Daniel Zerbino zerbino at ebi.ac.uk
Thu May 21 15:02:12 BST 2015

Wait a minute, *none* of them do? That's something else entirely...

Now, ExAC is a somewhat biased set in that it is pulled down from exon 
sequencing, and a difference between the old and the new build is that 
regions with the histone marks associated to transcription are no longer 
annotated as "regulatory". This is what you see at your locus 1:13372, 
on e75, where there used to be mostly "gene associated" annotations 
across cell types.

However, 0 hits across 10M sounds very suspicious. For example, the 
locus you describe happens to be on the edge of a CTCF feature (the 
actual binding site is a bit farther on the 5'), so it should 
technically have been reported.

We'll investigate...

On 5/21/15 1:56 PM, Konrad Karczewski wrote:
> 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...
> -Konrad
> On Thu, May 21, 2015 at 2:17 AM, Daniel Zerbino <zerbino at ebi.ac.uk 
> <mailto: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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