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Good afternoon -</div>
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I recently ran across a variant annotation from VEP that did not provide any SIFT annotation.</div>
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1: <span style="font-family: Menlo; font-size: 11px;">103343580 C > A (GRCh 37 coordinates)</span></div>
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<div><font face="Calibri,sans-serif">In dbNSFP, and by directly querying the most recent download of the SIFT scores from SIFT (</font><a href="http://sift.bii.a-star.edu.sg/sift4g/public/Homo_sapiens/GRCh37.74.zip" style="color: rgb(0, 0, 0); font-family: Menlo; font-size: 11px;">http://sift.bii.a-star.edu.sg/sift4g/public/Homo_sapiens/GRCh37.74.zip</a><font face="Menlo" size="2">)
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.</font></div>
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<div><font face="Menlo" size="2">Thanks for your thoughts -</font></div>
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<div><font face="Menlo" size="2">Ann</font></div>
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<span style="font-weight:bold">From: </span><<a href="mailto:dev-bounces@ensembl.org">dev-bounces@ensembl.org</a>> on behalf of Ann Black-Ziegelbein <<a href="mailto:elizabeth-black@uiowa.edu">elizabeth-black@uiowa.edu</a>><br>
<span style="font-weight:bold">Reply-To: </span>Ensembl developers list <<a href="mailto:dev@ensembl.org">dev@ensembl.org</a>><br>
<span style="font-weight:bold">Date: </span>Tuesday, October 11, 2016 at 11:43 AM<br>
<span style="font-weight:bold">To: </span>Ensembl developers list <<a href="mailto:dev@ensembl.org">dev@ensembl.org</a>><br>
<span style="font-weight:bold">Subject: </span>Re: [ensembl-dev] Sift/Polyphen scores from VEP cache vs. dbNSFP<br>
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<div>Thanks so much :)</div>
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<div>Ann</div>
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<span style="font-weight:bold">From: </span><<a href="mailto:dev-bounces@ensembl.org">dev-bounces@ensembl.org</a>> on behalf of Anja Thormann <<a href="mailto:anja@ebi.ac.uk">anja@ebi.ac.uk</a>><br>
<span style="font-weight:bold">Reply-To: </span>Ensembl developers list <<a href="mailto:dev@ensembl.org">dev@ensembl.org</a>><br>
<span style="font-weight:bold">Date: </span>Tuesday, October 11, 2016 at 11:35 AM<br>
<span style="font-weight:bold">To: </span>Ensembl developers list <<a href="mailto:dev@ensembl.org">dev@ensembl.org</a>><br>
<span style="font-weight:bold">Subject: </span>Re: [ensembl-dev] Sift/Polyphen scores from VEP cache vs. dbNSFP<br>
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Dear Ann,
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<div class="">you can find version information in the following file of your cache file directory:</div>
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<div class="">~/.vep/homo_sapiens_merged/84_GRCh37/info.txt</div>
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<div class="">Assuming you use ~/.vep to store your cache files.</div>
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<div class="">source_polyphen<span class="Apple-tab-span" style="white-space:pre"></span>2.2.2</div>
<div class="">source_sift<span class="Apple-tab-span" style="white-space:pre"> </span>
sift5.2.2</div>
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<div class="">We provide more information on how we run SIFT and PolyPhen here:</div>
<div class=""><a href="http://www.ensembl.org/info/genome/variation/predicted_data.html#sift" class="">http://www.ensembl.org/info/genome/variation/predicted_data.html#sift</a></div>
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<div class="">HTH,</div>
<div class="">Anja</div>
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<div class="">On 11 Oct 2016, at 17:24, Black-Ziegelbein, Elizabeth A <<a href="mailto:elizabeth-black@uiowa.edu" class="">elizabeth-black@uiowa.edu</a>> wrote:</div>
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Hello -</div>
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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 <span style="font-family: Menlo; font-size: 11px;" class="">homo_sapiens_merged/84_GRCh37</span>).
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?</div>
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For example:</div>
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Missense variant 6:33143391:G>A has no SIFT scores available for any transcript from the VEP annotation. <font face="Calibri,sans-serif" class="">From dbNSFP 3.1, the same variant has the following SIFT scores: 0.285;0.29;0.307 for the following transcripts:
</font><font face="Calibri,sans-serif" class="">ENST00000374708;ENST00000341947;ENST00000361917.</font></div>
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Thanks so much,</div>
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Ann </div>
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mailing list </span><a href="mailto:Dev@ensembl.org" style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class="">Dev@ensembl.org</a><br style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class="">
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