they were called with the same genotype, (ii) the distance between them was covered by <100 probes with a density > 0.2 probe per kb, (iii) the ratio of the number of probes between them to the number of probes of the merged call<0.1 and (iv) the difference in average log2ratio <0.15. Affy6 SNPs of all cases, controls, the HapMap1 populations (CEU, CHB+JPT, YRI) and an Indian population in HapMap3 (GIH) were called using Birdseed.
