plinkQC is a R/CRAN package for genotype quality control including a pre-trained ancestry classifier and relatedness filter optimized to retain the maximally unrelated sample set with highest quality.
plinkQC generates a per-individual and per-marker quality control report. A step-by-step guide on how to run these analyses can be found here. Individuals and markers that fail the quality control can subsequently be removed with plinkQC to generate a new, clean dataset.
The current github version of plinkQC is: 1.1.0 and can be installed via
library(devtools)
# install_github("meyer-lab-cshl/plinkQC")
install.packages("plinkQC", repos = c('https://meyer-lab-cshl.r-universe.dev', 'https://cloud.r-project.org'))
The current CRAN version of plinkQC is: 1.1.0 and can be installed via
install.packages("plinkQC")
A log of version changes can be found here.
Maha Syed, Caroline Walter, Hannah V Meyer, plinkQC: an integrated tool for ancestry inference, sample selection, and quality control in population genetics, Bioinformatics, Volume 42, Issue 9, September 2026, btag612, https://doi.org/10.1093/bioinformatics/btag612