[ensembl-dev] Ensembl-Condel Scoring

[Graham Ritchie]

Hi Paige,

We compute the Condel prediction using only the SIFT and PolyPhen scores, so there aren't any other factors it can use. I am also surprised by this prediction though so I have contacted the Condel authors to check what they make of it. I will let you know what they say.

Cheers,

Graham


On 2 Jun 2011, at 01:32, Paige Taylor wrote:

> Hi, 
> 
> I've been using the Variant Effect Predictor script but am confused by the Condel Score.  The Ensembl Variation webpage documents the Condel score as this:
> 
> " The Condel authors provided us with a version specialised for finding a consensus between SIFT and PolyPhen and we integrated this into the variation API."
> 
> However, I have noticed several examples of variant annotations where the Condel score is deleterious when both SIFT & Polyphen are tolerated/benign.  For example: 
> SIFT=tolerated(0.13);PolyPhen=benign(0);Condel=deleterious(0.871)
> (variant 1_1263085_G/A)
> 
> This leads me to believe that Condel is taking other factors into consideration besides just the Polyphen and SIFT score..do you have any information about this?
> 
> Thanks,
> 
> Paige  Taylor
> 
> Paige Taylor
> sptaylor at ucla.edu
> Graduate Student Researcher
> Stanley Nelson Lab
> University of California, Los Angeles
> 
> 
> 
> 
> 
> 
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