Question: How to check new variants for functional effects?
1
gravatar for Amirosein
3.5 years ago by
Amirosein70
UBC, Vancouver, CA.
Amirosein70 wrote:

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 annovar • 723 views
ADD COMMENTlink modified 3.5 years ago by DG7.1k • written 3.5 years ago by Amirosein70

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

ADD REPLYlink written 3.5 years ago by RamRS25k
1
gravatar for DG
3.5 years ago by
DG7.1k
DG7.1k wrote:

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

ADD COMMENTlink written 3.5 years ago by DG7.1k
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