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Consider defaulting flat prior across genotypes #139

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timothymillar opened this issue Jun 30, 2022 · 0 comments
Open

Consider defaulting flat prior across genotypes #139

timothymillar opened this issue Jun 30, 2022 · 0 comments
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enhancement New feature or request low priority question Further information is requested

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@timothymillar
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Currently we default to a Bayesian approach informed by an expected inbreeding coefficient of zero. This works well if accurate inbreeding priors are specified but we can expect many people will ignore this parameter. With an inbreeding prior of zero we are implicitly favoring heterozygous genotypes (especially when there are many alleles). It may be better to default to a truly "neutral" prior in which all genotypes are equally likely (analogous to maximum likelihood). This can be achieved by calculating the prior probability of any genotype as 1/G where G is the total number of possible genotypes.

@timothymillar timothymillar added enhancement New feature or request low priority labels Jun 30, 2022
@timothymillar timothymillar self-assigned this Jun 30, 2022
@timothymillar timothymillar added the question Further information is requested label Jul 11, 2022
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