[ensembl-dev] Sift/Polyphen scores from VEP cache vs. dbNSFP

[Black-Ziegelbein, Elizabeth A]

Hello -

We are running a local installation of VEP (v84) and are running it with –offline and –cache parameters. Caches were installed with the VEP script (we did not use custom caches - using homo_sapiens_merged/84_GRCh37).  I have noticed in some cases the SIFT and Polyphen scores for transcripts are different than what is reported in dbNSFP3 for a variant.  I was wondering what version of SIFT and Polyphen scores are included in the pre–built caches or if there are thoughts on why they would be different.  Additionally is it the polyphen v2 score or polyphen?

For example:

Missense variant 6:33143391:G>A  has no SIFT scores available for any transcript from the VEP annotation.  From dbNSFP 3.1, the same variant has the following SIFT scores: 0.285;0.29;0.307  for the following transcripts:  ENST00000374708;ENST00000341947;ENST00000361917.

Thanks so much,

Ann
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mail.ensembl.org/pipermail/dev_ensembl.org/attachments/20161011/3315a4fe/attachment.html>