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 (
FST, missing data, tests of
Hardy–Weinberg equilibrium,
inbreeding coefficient
The coefficient of inbreeding of an individual is the probability that two alleles at any locus in an individual are identical by descent from the common ancestor(s) of the two parents.
The coefficient of inbreeding is: The probability that two ...
, etc.);
*
Linkage disequilibrium
In population genetics, linkage disequilibrium (LD) is the non-random association of alleles at different loci in a given population. Loci are said to be in linkage disequilibrium when the frequency of association of their different alleles is h ...
(LD) calculation;
*
Identity by descent
A DNA segment is identical by state (IBS) in two or more individuals if they have identical nucleotide sequences in this segment. An IBS segment is identical by descent (IBD) in two or more individuals if they have inherited it from a common a ...
(IBD) and
identity by state
A DNA segment is identical by state (IBS) in two or more individuals if they have identical nucleotide sequences in this segment. An IBS segment is identical by descent (IBD) in two or more individuals if they have inherited it from a common an ...
(IBS) matrix calculation;
*
population stratification
Population structure (also called genetic structure and population stratification) is the presence of a systematic difference in allele frequencies between subpopulations. In a randomly mating (or ''panmictic'') population, allele frequencies are ...
, such as a
Principal component analysis;
* association analysis such as
genome-wide association study
In genomics, a genome-wide association study (GWA study, or GWAS), also known as whole genome association study (WGA study, or WGAS), is an observational study of a genome-wide set of genetic variants in different individuals to see if any vari ...
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. 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.
* 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
External links
PLINK 1.07 homepagePLINK 1.9 homepage
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Bioinformatics software
Computational biology
Genetics software