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")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.
Syed M, Walter C and Meyer HV (2025) plinkQC: An Integrated Tool for Ancestry Inference, Sample Selection, and Quality Control in Population Genetics. [bioRxiv]