PLINK (genetic tool-set)

PLINK 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.
PLINK currently supports following functionalities:
Input and output files.
PLINK has its own format of text files (.ped) and binary text files (.bed) that serve as input files for most analyses. A .map accompanies a .ped file and provides information about variants, while .bim and .fam files accompany .bed files as part of the binary dataset. 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. With certain formats such as VCF, some information such as phase and dosage will be discarded.
PLINK has a variety of output files depending on the analysis. PLINK has the ability to output files for BEAGLE and can recode a .bed file into a VCF for analyses in other programs. Additionally, PLINK is designed to work in conjunction with R, and can output files to be processed by certain R packages.