How does imputation software calculate haploid alternate allele dosage from posterior probabilities for genotypes?
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4.4 years ago
curious ▴ 820

I am performing imputation with minimac

I get this result for one field

Genotype :                                                                                  0|1
Estimated Alternate Allele Dosage [P(0/1)+2*P(1/1)]:                                      0.929
Estimated Haploid Alternate Allele Dosage:                                          0.046,0.883
Estimated Posterior Probabilities for Genotypes 0/0, 0/1 and  1/1              0.111,0.848,0.041

I get that the Estimated Alternate Allele Dosage .929 is calculated by (.848 + 2*.041)

I don't get how they calculate haploid alternate allele dosage. Does anyone know?

impuation • 1.4k views
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