Once this first hurdle has been surpassed, the next step is to impute missing genotypes for each sample. As noted in Table 2 and in the previous discussion, a key step is to select an appropriate set of reference haplotypes. Different choices of reference panel can be assessed by masking a subset of the available genotypes and checking whether these can be recovered accurately. After a reference panel has been selected and imputation is complete a key issue is deciding which markers to take forward for analysis. Typically, not all markers can be well imputed and several different measures have been proposed to help identify well imputed markers. The simplest of these measures focus on the average probability that an imputed genotype call is correct – in this context, one might look for markers where genotypes are imputed with >90% certainty or so. We don't recommend these types of measures because they are not very meaningful when comparing markers with different allele frequencies (for example, if a marker has an allele frequency of <5%, it should be possible to achieve
