GTQC: Automated Genotyping Array Quality Control and Report

J Genomics. 2022 Feb 14;10:39-44. doi: 10.7150/jgen.69860. eCollection 2022.


Genotyping array is the most economical approach for conducting large-scale genome-wide genetic association studies. Thorough quality control is key to generating high integrity genotyping data and robust results. Quality control of genotyping array is generally a complicated process, as it requires intensive manual labor in implementing the established protocols and curating a comprehensive quality report. There is an urgent need to reduce manual intervention via an automated quality control process. Based on previously established protocols and strategies, we developed an R package GTQC (GenoTyping Quality Control) to automate a majority of the quality control steps for general array genotyping data. GTQC covers a comprehensive spectrum of genotype data quality metrics and produces a detailed HTML report comprising tables and figures. Here, we describe the concepts underpinning GTQC and demonstrate its effectiveness using a real genotyping dataset. R package GTQC streamlines a majority of the quality control steps and produces a detailed HTML report on a plethora of quality control metrics, thus enabling a swift and rigorous data quality inspection prior to downstream GWAS and related analyses. By significantly cutting down on the time on genotyping quality control procedures, GTQC ensures maximum utilization of available resources and minimizes waste and inefficient allocation of manual efforts. GTQC tool can be accessed at

Keywords: genotyping; microarray; quality control.