In this review, we have tried to provide readers with an intuition about why genotyping imputation methods work, describe their history in the context of genomewide association studies, and to summarize some examples of current uses of genotype imputation. For readers that are encouraged to attempt genotype imputation in their own samples, we would like to spend a few paragraphs summarizing important practical issues to consider when carrying out genotype imputation based analyses. In particular, we will focus on issues we have encountered when developing, implementing and supporting our Markov Chain Haplotyping (MACH) software package for haplotype estimation and genotype imputation. As with other analyses of genetic association data, we recommend that a standard set of quality filters should be used to exclude markers with poor quality genotypes. These quality filters typically flag markers that have low call rates, significant evidence for deviations from Hardy-Weinberg equilibrium, a large rate of discrepancies between duplicate genotypes, or evidence for non-Mendelian inheritance (67).
