used 97%, 4 used 98%, and 2 used 99%. The P-value used to denote deviation from HWE varied from 10−4 to 10−7, with only 1 study using P=5×10−20. Twenty-one reports used some additional stated criterion other than MAF, HWE and SNP call rate. Finally, in most reports the individual studies included in the respective meta-analyses retained data with high imputation quality, with variable quality thresholds and different software used for imputation.
