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?
Best,
Sylvia
