PODKAT - An R Package for Association Testing Involving Rare and Private Variants
This package provides an association test that is capable of dealing with very rare and even private variants. This is accomplished by a kernel-based approach that takes the positions of the variants into account. The test can be used for pre-processed matrix data, but also directly for variant data stored in VCF files. Association testing can be performed whole-genome, whole-exome, or restricted to pre-defined regions of interest. The test is complemented by tools for analyzing and visualizing the results.
This is the source code repository. The package can be installed from Bioconductor. Further information and installation instructions are also available from http://www.bioinf.jku.at/software/podkat/.