How to check new variants for functional effects?

Question

[Amirosein]

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

[Ram]

+1 - I have this question as well. I use a suite of web-based tools now and manually extract a consensus.

Answer 1

[DG]

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