plinkQC: An Integrated Tool for Ancestry Inference, Sample Selection, and Quality Control in Population Genetics

Syed, Maha, Walter, Caroline, Meyer, Hannah V (August 2026) plinkQC: An Integrated Tool for Ancestry Inference, Sample Selection, and Quality Control in Population Genetics. Bioinformatics. btag612. ISSN 1367-4803

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Abstract

MOTIVATION: Population genetic analyses rely on high quality datasets that pass rigorous controls for sample and marker quality. Many analyses also require additional processing including identification of ancestry and sample relatedness. A software package that addresses all these common, yet crucial tasks is missing. RESULTS: We have developed plinkQC, an R/CRAN package that combines these functionalities into a single software package with detailed vignettes for example applications. plinkQC determines the ancestry of study samples via a pre-trained random forest classifier that reaches 98% performance accuracy with just 5% of marker overlap between reference and user data. To obtain the maximal set of unrelated study samples, we developed a graph-based pruning method, taking both relationship estimates and sample quality into account. We demonstrate optimal sample selection on the 1000 Genomes project, where we retain an additional 71 samples compared to publicly available exclusion lists. Finally, plinkQC bundles these results together with per-individual and per-marker quality control checks into three simple functions and returns both the quality controlled data set and quality control report about each step of the analysis. AVAILABILITY: plinkQC is available as an R/CRAN package. The documentation and code are available on github: https://meyer-lab-cshl.github.io/plinkQC/ and https://github.com/meyer-lab-cshl/plinkQC_manuscript. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Item Type:	Paper
Subjects:	bioinformatics bioinformatics > genomics and proteomics
CSHL Authors:	Meyer, Hannah V. Syed, Maha Walter, Caroline
Communities:	CSHL labs > Meyer Lab School of Biological Sciences > Publications
SWORD Depositor:	CSHL Elements
Depositing User:	CSHL Elements
Date:	14 August 2026
Date Deposited:	02 Sep 2026 19:44
Last Modified:	02 Sep 2026 19:44
Related URLs:	Publisher
URI:	https://repository.cshl.edu/id/eprint/42303

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