PLINK protocols

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PLINK computational protocol

PLINK specifications

Information


Unique identifier OMICS_00206
Name PLINK
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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Maintainer


  • person_outline Shaun Purcell <>

Publication for PLINK

PLINK IN pipelines

 (186)
2018
PMCID: 5759835
PMID: 29316879
DOI: 10.1186/s12864-017-4365-3

[…] 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 […]

2018
PMCID: 5804026
PMID: 29391395
DOI: 10.1038/s41398-017-0079-1

[…] 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 […]

2018
PMCID: 5804026
PMID: 29391395
DOI: 10.1038/s41398-017-0079-1

[…] p-value was selected from each of the ld-clumped snp sets. where two or more snps from a set had the same p-value, the snp with the larger beta coefficient was used. the scores were calculated in plink to produce a per-allele weighted score (without mean imputation). using stata, deciles of scores were computed and modelling the effect of the prs on risk was adjusted for age, sex, chip […]

2018
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) [44] and verified by eigensoft’s smartpca (version 3.0) [45]., annotation of the variants in genes set related to cardiovascular diseases were carried out using the clinvar […]

2018
PMCID: 5826192
PMID: 29515573
DOI: 10.3389/fimmu.2018.00242

[…] the amplicon regions covered in our ampliseq approach using vcftools (52) and for a maf > 0.05 using the genomeanalysistoolkit (gatk v. 3.2) (53, 54). the filtered snp list was then pruned using plink (55) 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 (51) to define […]

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

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