Roakvar is an R package for genomic variant analysis. It is an R wrapper for OakVar, a Python-based genomic variant analysis platform (OakVar is in turn further developed from OpenCRAVAT).
Without leaving the RStudio, VCF files can be annotated and the result can be pulled into an R data frame, for example.
See https://github.com/rkimoakbioinformatics/roakvar for Roakvar installation and usage, including the example.
See https://oakvar.readthedocs.io for OakVar installation and usage.
All CLI commands of OakVar is available as R functions through Roakvar, including a GUI server.
Comments and feedback are welcome.