Imputation from the Illumina Human-1M-duo array was simulated by masking all genotypes at SNPs (in the 50Mb simulated region) not present on the array followed by imputation at all polymorphic loci identified in the European samples of the 1000 Genomes Project phase 1 dataset using the remaining reference panel of haplotypes (381 in total). We used the MaCH27 imputation software with default parameters “--rounds 40 --greedy --mle --mldetails”.
