HAPMIX : interpretation of the 16 probabilities generated when run in DIPLOID mode
I am running the HAPMIX software for local ancestry estimation. When I run it in diploid mode, I get a 16 column output corresponding to the genotype and ancestry combinations. I am not able to understand the order in which these probabilities are given. Can somebody please help me understand what do the columns mean (in order?) Also, I am noticing some of the columns are identical (Like V2==V5; V8==V14, V4==V13). Can somebody help me with this?
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