I would to like do QTL mapping using genotypes of a F2 mouse generation which was derived by intercrossing from F0. F0 consists of individuals from two homozygous strains x and y. In my genotype file each marker has AA, AB or BB as possible genotype. However, allele A is not necessarily from strain x and allele B not necessarily from strain y.
Now, I am not sure if I have two switch the alleles accordingly to make sure that A is always from strain x and B is always from strain y.
If I understood right, in QTL mapping the correlation between the markers and and the phenotype is measured. However, what is not clear to me is if this done for each marker is correlated independently (which would not require that A is always from strain x and B is always from strain y) or not.