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PLINK specifications


Unique identifier OMICS_00206
Software type Package/Module
Interface Command line interface
Restrictions to use None
Input data Raw genotypes
Operating system Unix/Linux, Mac OS, Windows
Computer skills Advanced
Version 1.9
Stability Stable
Maintained Yes




No version available



  • person_outline Shaun Purcell

Publications for PLINK

PLINK citations


A joint view on genetic variants for adiposity differentiates subtypes with distinct metabolic implications

Nat Commun
PMCID: 5956079
PMID: 29769528
DOI: 10.1038/s41467-018-04124-9

[…] matter from which trait the SNP was derived). The “traits of a region” were defined as the union of traits contributing with genome-wide significance across the SNPs of the respective region. We used PLINK and EasyStrata for the clumping and for the comparison across traits. Of note, our clumping strategy will yield a different number of independent signals compared with the two GIANT studies that […]


Genetic variant for behavioral regulation factor of executive function and its possible brain mechanism in attention deficit hyperactivity disorder

Sci Rep
PMCID: 5956073
PMID: 29769613
DOI: 10.1038/s41598-018-26042-y
call_split See protocol

[…] Association analysis for each quantitative trait was conducted using an additive model in linear regression in PLINK with age, IQ, sex and eigenvector 1 of PCA as covariates. Two-sided P < 5 × 10−8 was considered as genome-wide significance. We used MACH-admix 1.0 to impute non-genotyped SNPs using the ASN dat […]


Polygenic pleiotropy and potential causal relationships between educational attainment, neurobiological profile, and positive psychotic symptoms

PMCID: 5954124
PMID: 29765027
DOI: 10.1038/s41398-018-0144-4
call_split See protocol

[…] es. We removed ~45,000 SNPs on the X or Y chromosome, minor allele frequency <0.05, call rate <98%, and P < 1 × 10E−6 for deviation from Hardy–Weinberg equilibrium. The QC steps were carried out with PLINK and resulted in a total of 374 subjects with genotype data on 664,907 autosomal SNPs.We then performed genotype imputation, using the phased haplotypes from the 1000 Genomes Project dataset as t […]


Thirty loci identified for heart rate response to exercise and recovery implicate autonomic nervous system

Nat Commun
PMCID: 5955978
PMID: 29769521
DOI: 10.1038/s41467-018-04148-1

[…] set into discovery (N ~ 40,000) and replication (N ~ 27,000) datasets (Fig. ). For the discovery data set, we selected the model SNPs from the genotyped SNPs, required for the subsequent GWASs using PLINK 1.9. This selection was based on the following criteria: a minor allele frequency (MAF) > 1%, a Hardy–Weinberg equilibrium (HWE) with a threshold of P-value = 1 × 10−6, and missingness < 0.0015. […]


Cross ancestry genome wide association analysis of corneal thickness strengthens link between complex and Mendelian eye diseases

Nat Commun
PMCID: 5951816
PMID: 29760442
DOI: 10.1038/s41467-018-03646-6

[…] late linkage disequilibrium (LD) patterns. We used the software GTOOL-v0.7.5 ( to convert BMES IMPUTE2 data (both SNPs and Indels) to the plink format. This conversion changes A/T/G/C/I/D/R based allele coding to 1 or 2 (first and second allele). We extracted variant IDs, hg19 genomic locations and converted A/T/G/C/I/D/R (from 1/2 base […]


Global genetic differentiation of complex traits shaped by natural selection in humans

Nat Commun
PMCID: 5951811
PMID: 29760457
DOI: 10.1038/s41467-018-04191-y
call_split See protocol

[…] UR and EAS samples (Supplementary Table ). In summary, ~6.1 million SNPs in 1000G and ~5.8 million SNPs in GERA after QC were used in the subsequent analyses.We used the LD-based clumping approach in PLINK to select trait-associated SNPs from GWAS summary data. The clumping approach filters out SNPs with P-values larger than a specific threshold, clusters the remaining SNPs by LD and physical dist […]


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PLINK institution(s)
Center for Human Genetic Research, Massachusetts General Hospital, Boston, MA, USA

PLINK review

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Anonymous user #108

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Most comprehensive and efficient GWAS toolkit.