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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.


GWAS study


  • Operation: Genetic variation analysis
  • Software interface: Command-line user interface
  • Language: C++, C
  • Operating system: Linux; Mac OS X
  • License: GNU GPL v2
  • Cost: Free
  • Version name: 1.9
  • Maturity: Mature
  • Credit: -
  • Contact: plink _at_ | shaun _at_
  • Collection: -


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
PMID: 17701901
PMCID: PMC1950838

Slifer SH "PLINK: Key Functions for Data Analysis." Curr Protoc Hum Genet. 2018 Apr;97(1):e59.
PMID: 30040203

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