I am trying to determine association between a set of haplotypes (2 or 3 marker SNPs) with a clinical outcome. I have phased the haplotypes using Phase v2.1.1 and calculated OR, p values using a 2x2 Fisher's exact test.
My supervisor says that I should be considering the reference haplotype (major allele frequency) and fixing the OR=1. I managed to do this using several software such as R (haplo.stats) and Unphased, which provide an option to set the reference haplotype.
However, I do not think that these software phase the haplotypes at all. Is it common to do both - phased haplotypes and set a reference group? I have seen several articles with methods that describe one or the other but not both at the same time. What is the convention and what software would be suitable?