PLINK is a popular and well-documented tool for the association and population-based linkage analyses for genome-wide association studies (GWAS). The PLINK package contains functions for data management, summary statistics for quality control, population stratification detection, association analysis, identity-by-descent estimation, and more. See also gPLINK, a GUI tool written in Java for PLINK.
Purcell S, Neale B, Todd-Brown K, Thomas L, Ferreira MA, Bender D, Maller J, Sklar P, de Bakker PI, Daly MJ, Sham PC "PLINK: a tool set for whole-genome association and population-based linkage analyses." Am. J. Hum. Genet. 2007; 81(3):559-75 https://doi.org/10.1086/519795
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