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PLINK is a free, Open source whole genome association analysis toolset, designed to perform a range of basic, large-scale analyses in a computationally efficient manner. It's managed by Broad Institute.

The focus of PLINK is purely on analysis of genotype/phenotype data (GWAS). Through integration with gPLINK and Haploview, there is some support for the subsequent visualization, annotation and storage of results.

Data input

  • PLINK 1 binary (.bed)
  • PLINK text (PED, .map, .tped,...)
  • VCF
  • 23andMe text

주요 기능들 #

  • Data management
  • Basic statistics
  • Linkage disequilibrium
  • Distance matrices
  • Identity-by-descent
  • Population stratification
  • Association analysis (GWAS)
  • Family-based association
  • Report postprocessing
  • Epistasis
  • Allelic scoring

Pairwise IBD estimation #

$ plink --genome full

모든 개체의 조합에 대해 IBD 추정함

IBS clustering #

$ plink --cluster

IBS로 군집분석 하고, 클러스터별 결과 제공

관련 정보 #


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