I have genotyping data of two SNPs obtained for cases and controls related to iron deficiency. I wanted to get the haplotype effect of those two SNPs, and therefore, I performed a haplotype based case-control association (--hap-assoc) and obtained a significant difference (P < 0.05) in cases and controls in the frequency of two haplotypes computed by the software. Then I performed the logistic regresion analysis (--hap-logistic) and obtained the odds ratios. Sliding Window specification was used for analyses. I am not clear if they have used a reference haplotype to compute the odds ratios and if so, what could be haplotype selected as the reference?
Hope I explained my questions clearly. Any input from people experienced with genetic analyses would more than welcome. Thank you very much!