PLINK (genetic tool-set)

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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.

PLINK currently supports following functionalities:

• data management;
• basic statistics (F_ST, missing data, tests of Hardy–Weinberg equilibrium, inbreeding coefficient, etc.);
• Linkage disequilibrium (LD) calculation;
• Identity by descent (IBD) and identity by state (IBS) matrix calculation;
• population stratification, such as a Principal component analysis;
• association analysis such as genome-wide association study for both basic case/control studies and quantitative traits;
• tests for epistasis