PLINK protocols

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chevron_left Association mapping Pathway analysis Joint association Single SNP association IBD segment detection Genotype imputation chevron_right
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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



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  • person_outline Shaun Purcell <>

Publications for PLINK

PLINK in pipelines

PMCID: 5758599
PMID: 29354142
DOI: 10.3389/fpls.2017.02185

[…] of 3–8 and selected a case for imputation with a max position/sample missingness of 0.70, a minimum depth of 5, and an imputation accuracy of 94.9%. the vcf was converted to a genotype table using plink v1.07 (purcell et al., ; purcell, )., of the 869 accessions assessed in this study, 816 had genomic data following imputation and filtering and were included in downstream analyses. […]

PMCID: 5805289
PMID: 29420653
DOI: 10.1371/journal.pone.0192446

[…] were prioritized. likewise, the relatedness of the populations based on the deleteriousness they harbored for cardiovascular diseases was assessed by principal component analysis (pca) using the plink tool (v1.90b3.30) [] and verified by eigensoft’s smartpca (version 3.0) []., annotation of the variants in genes set related to cardiovascular diseases were carried out using the clinvar data […]

PMCID: 5826192
PMID: 29515573
DOI: 10.3389/fimmu.2018.00242

[…] for the amplicon regions covered in our ampliseq approach using vcftools () and for a maf > 0.05 using the genomeanalysistoolkit (gatk v. 3.2) (, ). the filtered snp list was then pruned using plink () in order to exclude less informative snps in linkage disequilibrium (ld). a total of 161 resulting snps from the reference populations were then used as input for laser () to define the pca […]

PMCID: 5828093
PMID: 29607327
DOI: 10.1155/2018/9425843

[…] allele frequency (maf) < 0.01 were categorized as rare variants and variants with maf ≥ 0.01 were categorized as common variants., the association analysis of common variants was performed using plink []. we excluded variants from the association test that were either monomorphic, had a minor allele frequency (maf) < 0.05, or were missing in 95% of all subjects. we used the false […]

PMCID: 5844309
PMID: 29343494
DOI: 10.1534/g3.117.300493

[…] of p-values closest to a uniform distribution (figure s1). an ld threshold of r2 < 0.01 was chosen and yielded a set of 63 snp groups centered around a representative snp or “index variant” (plink; ) shown in table s2. the resulting manhattan plot and the corresponding histogram of p-values are displayed in figure s1c. as shown across figure s1, accounting for ld facilitated detection […]

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PLINK in publications

PMCID: 5956073
PMID: 29769613
DOI: 10.1038/s41598-018-26042-y

[…] preprocessing and quality control detailed is described in the supplementary material., 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 […]

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

[…] ~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 […]

PMCID: 5951811
PMID: 29760457
DOI: 10.1038/s41467-018-04191-y

[…] maf and ld on segment #1 (some of which were under background selection because of the ld with deleterious mutations)., gcta:, slim:, plink:, aric data:, gera data: […]

PMCID: 5946424
PMID: 29747566
DOI: 10.1186/s12864-018-4749-z

[…] identity across multiple sequencing runs was confirmed by assessment of identity-by-descent at snps included on the 170 k illumina hd canine snp array. ibd across all runs was calculated using the plink --genome function []. we removed samples with sequencing runs (> 100,000 reads) that displayed a low level of relatedness across runs (pi-hat < 0.90) to avoid merging runs derived […]

PMCID: 5940788
PMID: 29739929
DOI: 10.1038/s41467-018-04086-y

[…] estimated to be genetically related, and 439 individuals showing signs of insufficient data quality, resulting in 121,296 individuals (supplementary table )., logistic regression was performed using plink (version 1.90 b3.38) assuming an additive genetic model and including sex as covariate, as well as the first five principal components assessed on the genomic data to control for potential […]

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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.