Appendix S1 - Reliable Single Chip Genotyping with Semi-Parametric Log-Concave Mixtures

We describe the translation step to match HapMap genotype calls to the SCALA {AA, AB, BB} format. We compare genotype calls to those of Phase III. We only compare calls to SNPs that have matching ‘RSid's. almost half of the total. We disregard the four allelotypes (A,C,G,T) and refer to homozygous genotypes as AA or BB and the heterozygous as AB. Since genotype calls AA from either method are highly unlikely to be mistaken for BB, we can apply the above forced classification from the HapMap homozygous genotype calls into homozygous calls from SCALA. (PDF)