How to check new variants for functional effects?
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7.8 years ago
Amirosein ▴ 70

Hi all

I'm writing a code in Rstudio/Bioconductor and i found some unreported variations from some patients, is there any easy way to predict functional effects of this changes? any package? specially i want to check them for pathogeneticity(?), like what SIFT and PolyPhen2 do, but inside Rstudio or any other programming enviroment.

thanks

variants snp SNP annovar • 1.3k views
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+1 - I have this question as well. I use a suite of web-based tools now and manually extract a consensus.

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7.8 years ago
DG 7.3k

You can do standard annotations of VCF files themselves though. You can use snpEff with its snpsift module to add annotations from dbNSFP predictions. This shouls give you at least a few of predictions from SIFT, polyphen, etc. You can combine this with https://gemini.readthedocs.io/en/latest/ to add additional ones such as GERP++, CADD, etc.

There are probably a whole host of other tools for doing this outside of R/bioconductor just working at the level of VCF files.

If you really want to stick within R/bioconductor I think you can access ensemblVEP to annotate your variants, and that should include a bunch of the functional effect predictors you are interested in. See here

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