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 #

논문

• sPLINK: A Federated, Privacy-Preserving Tool as a Robust Alternative to Meta-Analysis in Genome-Wide Association Studies bioRxiv 2020-06-06
• BLINK: A Package for Next Level of Genome Wide Association Studies with Both Individuals and Markers in Millions bioRxiv 2017-11-30: Big data 시대의 GWAS 도구로 PLINK와 비교하여 BLINK 프로그램 리뷰

Incoming Links #

Related Medical Scholarly Articles (MedicalScholarlyArticle 0) #

• Complex disease and phenotype mapping in the domestic dog
• Robust relationship inference in genome-wide association studies

Related Articles (Article 1) #

• Best linear unbiased prediction
• Bioinformatics
• F-statistics
• Identity by descent
• SNV

Related Software Applications (SoftwareApplication 2) #

• GenomeStudio
• KING

Related Codes (Code 3) #

• Haploview

Suggested Pages #

• 0.318 Large language model
• 0.151 IBD
• 0.105 Breeding value
• 0.067 Crohn's disease
• 0.033 SNP
• 0.024 Bioinfo-Bloggers
• 0.023 BioPerl
• 0.022 United States
• 0.021 Translational bioinformatics
• 0.020 장혜식
• More suggestions...