PLINK (genetic tool-set)

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

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.^[2] 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.^[3]
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.
^ 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.

External links

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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] 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

[3] 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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