These include, but are not limited to [5], evaluation of Hardy-Weinberg equilibrium, missing rate, and, in the case of imputed variants, imputation accuracy scores. Rules should be set upfront on what thresholds are not acceptable for each such quality check (e.g. p<0.0001 for Hardy-Weinberg violation, call rate <95%, or imputation accuracy <90%). Such quality checks may help reduce the impact of genotyping and other errors.
