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
3.5 years ago by
DG ♦ 7.1k