Hello,
I am doing SNP analysis for my gene. I have calculated SIFT and Polyphen score but I cannot find way to calculate REVEL score. Can someone guide me, how can I get this score?
Thank you.
Hi Khushbukhat,
You can use tools as VEP (http://asia.ensembl.org/index.html ) and either running their web interface or stand-alone apps.
Another option is to download and run dbNSFP (https://sites.google.com/site/jpopgen/dbNSFP ) by either using their have script or your own script. I prefer the second options as dbNSFP has all in-silico prioritisation algorithms (over 100).
Hope it helps, Pawel
Hello,
You can calculate it inputting their SNP id in: https://sites.google.com/site/revelgenomics/.
I would also highly recommend looking at your SNPs in other predictors like Clinvar, FATHMM, clinpred etc... Normally it is recommended to use the highest number of possible predictors since only SIFT and Polyphen scores are not enough. If you want to read more about in silico predictions the group I am a part of wrote a short letter about it last year: Article Candidate genes identified by whole-exome sequencing in pree...
Thank you Pawel Suwinski for the answer. I checked VEP, it did not give result for my the SNPs in my gene. dbNSFP is working great. Thank you
Izabela Mamede C A Conceição ... Thank you for your response. Your paper is not public. Can you share with me?
Can you suggest how many tools will be enough to validate deleterious SNPs in a gene?
Khushbukhat Khan Just sent the article to you using the messages function.
There is no exact number of predictors to use but the general medical guidelines (like 10.1038/gim.2015.30) recommend as many as you can. I would say to have confidence in your result, 4 or 5 which use different techniques to determine pathogenicity (conservation, machine learning etc...).
Khushbukhat Khan As I was typing the answer, ResearchGate suggested me an article with a very recent new predictor:
- 10.1186/s13073-020-00775-w
Dear Izabela Mamede C A Conceição ! Really appreciate your response. I will probe CAPICE and will read your article and let your know soon.
Thank you so much. Stay blessed.
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