PLINK (genetic tool set)

Updated on Dec 13, 2023

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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:

data management;

basic statistics;

Linkage disequilibrium (LD) calculation;

Identity by descent (IBD) and identity by state (IBS) matrix calculation;

population stratification;

association analysis such as Genome-wide association study for both basic case/control studies and quantitative traits.

Extensions and current developments

PLINK 2.0 a comprehensive update to PLINK, developed by Christopher Chang, with the improved speed of various Genome-wide association (GWA) calculations, including identity-by-state (IBS) matrix calculation, LD-based pruning and association analysis.

PLINK/SEQ is an open-source C/C++ library designed for analyzing large scale whole-genome and whole-exome studies.

MQFAM is a multivariate test of association (MQFAM) that can be efficiently applied to large population-based samples and is implemented in PLINK.

References

PLINK (genetic tool-set) Wikipedia

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