Closed congzhouczcz closed 4 years ago
This is a great question. As unsatisfying as it is, I would choose one individual to be the ancestral individual and use their alleles. The math assumes one outgroup individual. A single substitution or allele with a miscalled ancestral or derived allele will contribute much less to the Beta score than SNPs at highly similar frequencies do, so it shouldn't affect scores much.
Hey Katie, I want to known if I have more than one ancestral individuals with different allele state (G and T), which individual should I choose? Thanks, Cong