In general, the following QCs are performed at the preimputation stage: minor allele frequency (MAF) ≥1–5%, Hardy–Weinberg equilibrium (HWE) P-value >10−4–10−6, SNP call rate ≥90–99%, sample call rate ≥90–98%, and other checks such as sex mismatch and Mendelian errors. For the details of QCs in GWAS, we refer to Anderson et al.6 Imputation software such as MACH7 or IMPUTE8 can be used to impute SNPs based on the HapMap CEU-phased haplotypes. There seems to be no consensus yet on the QCs after imputation, and on reporting the quality of imputed genotypes in publications. In the tutorial of MACH an inclusion threshold r2 of 0.3 is recommended. In addition to the preanalysis information measures, such as r2 of MACH and info of IMPUTE, which are the information measures about the population allele frequency, SNPTEST8 provides a post-analysis information measure about the association parameter for unrelated samples. Here we propose a similar post-analysis information measure to test related samples, called RT2.
