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 <>

PLINK article

PLINK citations

PMCID: 5919379

[…] ofc cohort) genotyped and imputed snps with maf > 1%. for 3dfn, gwas was performed using linear regression while adjusting for sex, age, height, weight and four pcs of ancestry as implemented in plink [31]. for ofc, which included relatives, gwas was performed using a mixed-models approach as implemented in emmax, which explicitly models the variance due to the kinship (comprising […]

PMCID: 5863221

[…] (p < 0.001 per sample) were excluded (henn et al. 2011). we removed four hadza individuals and three sandawe individuals identified as 2nd degree or closer relatives using the –genome function in plink (purcell et al. 2007). all individuals had sample call rates >95%. we then integrated these data into our global data set of 3,528 unrelated individuals genotyped at 19,372 diallelic […]

PMCID: 5764334

[…] of association < 5 × 10−6., we confirmed the robustness of the results of the genetic association analysis with a linear model including six covariates from principal component analysis (methods, plink). again, only one locus exceeded genome-wide significance in association with shb (snp = rs11697300, p = 2.52 × 10−9). and again, the area around scl30a9 was revealed to be heavily populated […]

PMCID: 5759835

[…] estimated., the homozygous segments shared by more than 50% of the samples were chosen as an indication of possible roh islands throughout the genome. the --homozyg-group function implemented in plink v1.90 [84] was used to assess roh islands shared among individuals. the map viewer of the bovine genome umd3.1.1 was used for identification of genes in roh regions, available at “national […]

PMCID: 5696417

[…] by carson et al. (2014). this snp set, referred to as “filtered snps” hereafter, was used to estimate population genetics parameters., pairwise ld (r 2) between nuclear markers was calculated with plink 1.9 (purcell et al., 2007) for each gene that contained two or more filtered snps in the population. ld decay with physical distance within genes was estimated based on sample size (n) […]

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

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