Trio binning - 1 mother 2 possible fathers

[carolhsb]

Hi,

I´m using the Trio Binning strategy on a hybrid fish species. I know the ID of the mother, but I have two possible fathers.

I´m thinking of mixing the two fathers' DNA for short-reads extraction. Do you think this strategy can cause problems in separating the hybrid haplotypes?

Can you give me any tips or suggestions on how I should handle this problem?

Many thanks,

Carolina