The imputation output files are a set of genotype probabilities for all markers and ‘best-guess’ genotype hardcall files filtered on imputation quality and minor allele frequency. Hard call genotypes are available in three levels (hardcall with genotype probability >0.8, otherwise missing): (i) no further filter, (ii) lightly filtered (missingness <0.02) and (iii) filtered with strict criteria (missingness <0.01; MAF >5%).
