I have a yeast population bred by intercrossing the descendants of four founder strains. We have SNP data for the descendants, and the founders are fully sequenced.

I would like to discover QTL in this population. To account for the effects of population structure, at every SNP I need to find the probabilities that this SNP is inherited from each of the founder strains.

Is there a program that will do this for me? I have looked at various ancestry inference programs, and they all seem to assume that the founders are unknown and must be inferred from the population. We know the founders, so this seems like it would lead to a large loss of useful information.

I have also investigated Hidden Markov Models, where the hidden state would be the founder ancestry and the output would be the SNP. However, this problem seems like it would need a different emission matrix for every SNP, which is different from the single emission matrix in the standard model.

Thanks for any help,

Stephanie