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ksiewert / BetaScan

Genome-wide scan for balancing selection using beta statistic
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which ancestral individual should I choose? #5

Closed congzhouczcz closed 4 years ago

congzhouczcz commented 4 years ago

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

ksiewert commented 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.