[ensembl-dev] Sift scores from VEP

[Sarah Hunt]

Hi Ann,

Thanks for reporting this. Checking at this variant in GRCh38, SIFT 
scores are available for the protein coding transcripts which suggests 
the lack of scores for GRCh37 may be due to a technical issue. We will 
look into this when we next update our GRCh37 database.

Best wishes,

Sarah


On 01/02/2017 19:02, Black-Ziegelbein, Elizabeth A wrote:
> Good afternoon -
>
> I recently ran across a variant annotation from VEP that did not 
> provide any SIFT annotation.
>
> 1: 103343580 C > A  (GRCh 37 coordinates)
>
> In dbNSFP, and by directly querying the most recent download of the 
> SIFT scores from SIFT 
> (http://sift.bii.a-star.edu.sg/sift4g/public/Homo_sapiens/GRCh37.74.zip) 
> show this SNP as having a SIFT score of 0 – damaging.  It is a 
> missense variant.  I found the documentation about how SIFT and 
> Polyphen scores are computed by VEP – but just wanted to check/verify 
> that this should be expected and not some type of error? I have found 
> more than one instance of this.
>
> Thanks for your thoughts -
>
> Ann
>
>
> From: <dev-bounces at ensembl.org <mailto:dev-bounces at ensembl.org>> on 
> behalf of Ann Black-Ziegelbein <elizabeth-black at uiowa.edu 
> <mailto:elizabeth-black at uiowa.edu>>
> Reply-To: Ensembl developers list <dev at ensembl.org 
> <mailto:dev at ensembl.org>>
> Date: Tuesday, October 11, 2016 at 11:43 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
>
> 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_siftsift5.2.2
>
> 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
>> _______________________________________________
>> Dev mailing list Dev at ensembl.org <mailto:Dev at ensembl.org>
>> Posting guidelines and subscribe/unsubscribe 
>> info:http://lists.ensembl.org/mailman/listinfo/dev
>> Ensembl Blog:http://www.ensembl.info/
>
>
>
> _______________________________________________
> Dev mailing list    Dev at ensembl.org
> Posting guidelines and subscribe/unsubscribe info: http://lists.ensembl.org/mailman/listinfo/dev
> Ensembl Blog: http://www.ensembl.info/

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mail.ensembl.org/pipermail/dev_ensembl.org/attachments/20170202/802da3f4/attachment.html>