The genetic distance calculated for hapmap data counts ambiguous codes as a mismatch when it should be counted as no data, or at least, no mismatch. For example, if a base is scored as an "M", and it is compared to another individual with an "A" at the same position, it currently counts that as a mismatch, and it should not. When I compared two entries of the same genotype, the only differences in SNPs were some ambiguous codes, and the distance between the two entries was NOT zero, which it was after I changed all ambiguous codes to "N".
Hi Peter, can you route this to the right person? Even me if you think so. -Terry