We recommend removing or flagging any SNPs that have one or more Mendelian errors on HapMap control samples. While it may be possible to look for Mendelian inconsistencies using study samples, removing these SNPs could potentially be filtering out a phenotype specific copy number variant. If this is the case, there will likely be more than three genotype clusters. The extra clusters or parts of them will be missing or miscalled. For instance, for a locus with alleles A and B, A-, AA, and AAB may all cluster together unless the SNP is re-called with a specific model in mind.
