Aligning divergent species data

[inti]

Hi,
I have some data from inter-species hybrids. For the genus only a single specie has a reference genomes so some individuals (hybrids) will get their data aligned to a ref genome which is none of the parental species. This mean I expect great divergence to the ref genome.

Do you have any suggestions on parameters for MOSAIK on this case?

Thanks in advance