PLINK (genetic tool-set)

PLINK
PLINK
Developer(s)	Shaun Purcell; Christopher Chang (PLINK 1.9/2.0)
Initial release	2007
Stable release	1.9 / December 2015
Written in	C, C++
Operating system	Windows, macOS, Linux
Platform	Command-line interface
Available in	English
Type	Bioinformatics software
License	GNU General Public License
Website	www.cog-genomics.org/plink/

Last updated July 29, 2025

PLINK is a free, open-source whole-genome association analysis toolkit used to perform a wide-range of genetic data analysis. It was designed by Shaun Purcell and published in 2007.^[1]As of 2025^[update], it has been cited over 35,000 times and is considered to be one of the most used and most comprehensive^[2] programs for analyzing SNP genotypes from diverse genetic datasets in population genetics.^[3]

Overview

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

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.^[5] 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.

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.^[6]
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

↑ Purcell S; Neale B; Todd-Brown K; Thomas L; Ferreira MAR; Bender D; Maller J; Sklar P; de Bakker PIW; Daly MJ; Sham PC (2007). "PLINK: a toolset for whole-genome association and population-based linkage analysis". American Journal of Human Genetics. 81 (3): 559–75. doi:10.1086/519795. PMC 1950838 . PMID 17701901.
↑ Slifer, Susan H. (2018-01-01). "PLINK: Key Functions for Data Analysis". Current Protocols in Human Genetics.
↑ Meyermans, R.; Gorssen, W.; Buys, N.; Janssens, S. (2020-01-29). "How to study runs of homozygosity using PLINK? A guide for analyzing medium density SNP data in livestock and pet species". BMC Genomics.
↑ Chang, Christopher C; Chow, Carson C; Tellier, Laurent CAM; Vattikuti, Shashaank; Purcell, Shaun M; Lee, James J (2015-12-01). "Second-generation PLINK: rising to the challenge of larger and richer datasets". GigaScience.
↑ Christopher Chang (2017). "PLINK 1.9 File format reference" (PDF). Biobank UK at University of Oxford. Retrieved 2022-08-05. PLINK input and output file formats which are identifiable by file extension
↑ Lee, James J.; Purcell, Shaun M.; Vattikuti, Shashaank; Tellier, Laurent CAM; Chow, Carson C.; Chang, Christopher C. (2015-12-01). "Second-generation PLINK: rising to the challenge of larger and richer datasets". GigaScience. 4 (1): 7. doi: 10.1186/s13742-015-0047-8 . PMC 4342193 . PMID 25722852.

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[1] Purcell S; Neale B; Todd-Brown K; Thomas L; Ferreira MAR; Bender D; Maller J; Sklar P; de Bakker PIW; Daly MJ; Sham PC (2007). "PLINK: a toolset for whole-genome association and population-based linkage analysis". American Journal of Human Genetics. 81 (3): 559–75. doi:10.1086/519795. PMC 1950838 . PMID 17701901.

[2] Slifer, Susan H. (2018-01-01). "PLINK: Key Functions for Data Analysis". Current Protocols in Human Genetics.

[3] Meyermans, R.; Gorssen, W.; Buys, N.; Janssens, S. (2020-01-29). "How to study runs of homozygosity using PLINK? A guide for analyzing medium density SNP data in livestock and pet species". BMC Genomics.

[4] Chang, Christopher C; Chow, Carson C; Tellier, Laurent CAM; Vattikuti, Shashaank; Purcell, Shaun M; Lee, James J (2015-12-01). "Second-generation PLINK: rising to the challenge of larger and richer datasets". GigaScience.

[5] Christopher Chang (2017). "PLINK 1.9 File format reference" (PDF). Biobank UK at University of Oxford. Retrieved 2022-08-05. PLINK input and output file formats which are identifiable by file extension

[6] Lee, James J.; Purcell, Shaun M.; Vattikuti, Shashaank; Tellier, Laurent CAM; Chow, Carson C.; Chang, Christopher C. (2015-12-01). "Second-generation PLINK: rising to the challenge of larger and richer datasets". GigaScience. 4 (1): 7. doi: 10.1186/s13742-015-0047-8 . PMC 4342193 . PMID 25722852.

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