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Updated: Dec 30, 2025

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Data Management and Summary Statistics with PLINK.

Christopher C Chang1

  • 1GRAIL, Inc., Menlo Park, CA, USA. chrchang@alumni.caltech.edu.

Methods in Molecular Biology (Clifton, N.J.)
|January 25, 2020
PubMed
Summary
This summary is machine-generated.

PLINK is a versatile tool for genomic data management and quality control. It streamlines basic computations on genomic variant data, saving researchers time for advanced analyses.

Keywords:
Allele frequencyHardy–Weinberg equilibriumLinkage disequilibriumPrincipal component analysisRelationship inferenceSex inferenceVariant call format

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Area of Science:

  • Genomics
  • Bioinformatics
  • Computational Biology

Background:

  • Genomic variant data analysis requires efficient tools for data management and quality control.
  • Repetitive implementation of basic operations hinders advanced population genomics research.

Purpose of the Study:

  • To describe essential data management and quality control operations in PLINK.
  • To highlight the utility and potential pitfalls of these basic operations in population genomics.

Main Methods:

  • Utilizing the PLINK software for genomic data processing.
  • Demonstrating common data management and quality control functionalities.

Main Results:

  • PLINK provides efficient handling of genomic variant matrices.
  • Key operations for data quality and management are detailed with practical examples.

Conclusions:

  • PLINK serves as a foundational tool for population genomics.
  • Understanding PLINK's basic operations is crucial for accurate and efficient genomic research.