PLINK pipeline

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 <>

Publication for PLINK

PLINK citations

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: 5804026

[…] and p < 0.05. a score of only gwas significant snps was not conducted, as a 2 snp score (after linkage disequilibrium (ld)-based pruning) would be underpowered. ld pruning was performed via plink on a random sample of 10,000 individuals using an r2 > 0.05 in a 250 kb window. the snp with the lowest p-value was selected from each of the ld-clumped snp sets. where two or more snps […]

PMCID: 5863221

[…] et al. (2011) due to excessive relatedness to the ≠khomani individuals from schlebusch et al. (2012) already present in our global data set. data management and quality control were performed using plink version 1.07 (purcell et al. 2007). graphical and statistical analyses were performed using r (r core team 2013)., to investigate possible snp ascertainment bias, we used the –weir-fst-pop […]

PMCID: 5904126

[…] whole genome sequencing dataset of a chinese han sample (n = 1329) in our laboratory., individual snp-based association analysis was performed for both smoking status and ftnd score using plink (v. 1.07)44 under the logistic regression model. adjusted covariates included age, site (taiyuan or jincheng), number of smoking family members, and income. in the haplotype-based association […]

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 […]

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

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