plinkQC

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.

Installation

The current github version of plinkQC is: 2.0.0 and can be installed via

library(devtools)
install_github("meyer-lab-cshl/plinkQC")

The current CRAN version of plinkQC is: 1.0.0 and can be installed via

install.packages("plinkQC")

A log of version changes can be found here.

Citation

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