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

[Black-Ziegelbein, Elizabeth A]

Thanks so much :)

Ann

From: <dev-bounces at ensembl.org<mailto:dev-bounces at ensembl.org>> on behalf of Anja Thormann <anja at ebi.ac.uk<mailto:anja at ebi.ac.uk>>
Reply-To: Ensembl developers list <dev at ensembl.org<mailto:dev at ensembl.org>>
Date: Tuesday, October 11, 2016 at 11:35 AM
To: Ensembl developers list <dev at ensembl.org<mailto:dev at ensembl.org>>
Subject: Re: [ensembl-dev] Sift/Polyphen scores from VEP cache vs. dbNSFP

Dear Ann,

you can find version information in the following file of your cache file directory:

~/.vep/homo_sapiens_merged/84_GRCh37/info.txt

Assuming you use ~/.vep to store your cache files.

source_polyphen2.2.2
source_sift sift5.2.2

We provide more information on how we run SIFT and PolyPhen here:
http://www.ensembl.org/info/genome/variation/predicted_data.html#sift

HTH,
Anja


On 11 Oct 2016, at 17:24, Black-Ziegelbein, Elizabeth A <elizabeth-black at uiowa.edu<mailto:elizabeth-black at uiowa.edu>> wrote:

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
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