[ensembl-dev] Motif feature consequences discrepancy

[Anja Thormann]

Hi Sigurjon,

VEP only reports overlaps with 'experimentally verified’ motif features. Which means those motif features fully overlap with a relevant ChIP-Seq peak. On the website we are still showing overlaps with unverified motif features. This will be updated for next release 100 when we are only going to show overlaps with 'experimentally verified’ motif features. Our blog post <http://www.ensembl.info/2018/10/15/new-ensembl-motif-features/> gives more details on how we report motif features.

Best wishes,
Anja

> On 12 Mar 2020, at 12:53, Sigurjón Axel Guðjónsson <Sigurjon.Gudjonsson at decode.is> wrote:
> 
>  
> Hi,
>  
> I am using VEP r99 to annotate i.e. rs759323910, and I notice that VEP only annotates MotifFeature ENSM00524563717 (ENSPFM0379). 
> The web browser does hower annotate 2 MotifFeatures ENSM00524563717 (ENSPFM0588) and ENSM00489900360 (ENSPFM0379). 
>  
> See:
> http://www.ensembl.org/Homo_sapiens/Variation/Mappings?db=core;v=rs759323910;vdb=variation <http://www.ensembl.org/Homo_sapiens/Variation/Mappings?db=core;v=rs759323910;vdb=variation>
>  
> Is there any valid reason for this discrepancy or is this a bug in VEP r99?
>  
> Best regards,
>  
> Sigurjon A. Gudjonsson
> Bioinformatics Group
> Decode Genetics
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