incorrect automated genotype calling (at least with currently widely used algorithms). Even though such weight is placed on pre-imputation SNP QC, the effects of applying different criteria and thresholds to the starting dataset have not been investigated thus far. In this report, we evaluate the effect of GWAS QC on imputation outcome, and find that imputation works very well for common variants irrespective of QC, and that a minority of some common-frequency SNPs with particular properties cannot be accurately imputed regardless of QC stringency.
