PLINK[1] is a free, commonly used, open-source whole-genome association analysis toolset designed by Shaun Purcell.
The software is designed flexibly to perform a wide range of basic, large-scale genetic analyses.
Additionally, PLINK accepts inputs of VCF, BCF, Oxford, and 23andMe files, which are typically extracted into the binary .bed format prior to performing desired analyses.
PLINK has a variety of output files depending on the analysis.
Additionally, PLINK is designed to work in conjunction with R, and can output files to be processed by certain R packages.