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PLINK

Definition
AI-generated

PLINK is a free, open-source command-line toolkit for large-scale genotype data: format conversion, quality control, linkage disequilibrium, principal components, relatedness, association testing, clumping, and related post-processing.

Topics
GWAS
URL
https://www.cog-genomics.org/plink/
Related
BGEN Genome-Wide Association Study (GWAS) Genotype Dosage

Why it matters in GWAS

Many published pipelines and tutorials use PLINK flags and file conventions (e.g. .bed/.bim/.fam, --glm, --clump, --indep-pairwise, --make-king), so recognizing PLINK-specific terminology aids reproducing analyses and reading supplementary methods.

Example usage

"Genotypes were converted with PLINK 2, QC filters applied, and association tested with --glm including ancestry PCs as covariates."

BGEN Genome-Wide Association Study (GWAS) Genotype Dosage KING-Robust Kinship LD Clumping LD Pruning Polygenic Risk Score (PRS) PRSice-2 Mendelian Error Quality Control (QC)
Related-term network

Click any node to open that term page.

Node order. The current term is first. Next come every page linked from Related terms, in the same top-to-bottom order as that list. Then new terms appear in two-hop layers: for each of those direct neighbors (in that same order), their related terms are appended if not already listed. A third pass does the same for two-hop nodes. The walk stops when a fixed maximum number of nodes is reached.

References

  • Purcell S, et al. (2007). PLINK: a tool set for whole-genome association and population-based linkage analyses. Am J Hum Genet.
  • Chang CC, et al. (2015). Second-generation PLINK: rising to the challenge of larger and richer datasets. Gigascience. https://doi.org/10.1186/s13742-015-0047-8
  • PLINK 2.0 documentation: https://www.cog-genomics.org/plink/2.0/
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