IPGWAS: An integrated pipeline for rational quality control and association analysis of genome-wide genetic studies

► Identifies rational quality control thresholds for genome-wide association study. ► Calculates Cochran-Armitage trend test p value for different genetic model. ► Calculates Pearson's χ2 test p value for different genetic model. ► Manhattan plot and QQ plot for the genome-wide association study results. ► Data manipulation and converting format for popular genetic software.