[ensembl-dev] Discrepancies between VEP and Condel, PPH2 and SIFT
A. P. Levine
a.levine at ucl.ac.uk
Thu Feb 2 12:14:08 GMT 2012
I have noticed some discrepancies between the PolyPhen, SIFT and Condel scores as reported by the VEP compared with the scores reported by the three programs independently.
The variant I have been looking at is "chr7: 140501302 T/C" (build 37).
Using the VEP (either online or with the perl script):
PolyPhen benign 0.382
Condel neutral 0.418
SIFT tolerated 0.09
Using the Condel server (http://bg.upf.edu/condel/analysis):
Condel 0.673 deleterious
Using SIFT (http://sift.jcvi.org/www/SIFT_chr_coords_submit.html):
SNP Type Nonsynonymous
SIFT Score 0.04
Median Information Content 2.93
And finally, using PolyPhen-2 with both HumDiv and HumVar classifier models (http://genetics.bwh.harvard.edu/pph2/bgi.shtml):
HumVar possibly damaging pph2_prob 0.791
HumDiv possibly damaging pph2_prob 0.942
What do you think might be happening here? Which versions of the various programs are being used by the VEP?
Adam P. Levine
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