[ensembl-dev] Ensembl-Condel Scoring

[Paige Taylor]

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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