Determine the derived allele

Question

[Jautis]

Hi, I'm working in a non-model primate and we have an assembled genome comprised of various scaffolds. We sequenced a population of individuals and would like to determine which is the derived vs ancestral allele.

Conceptually, this is simply using an outgroup (in this case, the best choice is the rhesus macaque) to determine the likely ancestral allele. However, it's not clear how to transfer calls from the macaque genome over to our assembly to determine the ancestral allele. Any suggestions about an efficient way to do this?

Thanks in advance!