Changes

Minimac3 estimates imputed dosage at an haplotype level by finding the posterior probability of the alternate allele at that site. The genotype dosage is next evaluated as the sum of the haplotype dosages of each haplotype. For e.g. if the estimated posterior probability of the alternate allele is 0.98 and 0.96 in each haplotype, the genotype dosage is output as 0.98 + 0.97 = 1.95.

Minimac3 estimates imputed dosage at an haplotype level by finding the posterior probability of the alternate allele at that site. The genotype dosage is next evaluated as the sum of the haplotype dosages of each haplotype. For e.g. if the estimated posterior probability of the alternate allele is 0.98 and 0.96 in each haplotype, the genotype dosage is output as 0.98 + 0.97 = 1.95.

= '''Hard Genotype''' =

= '''Hard Genotype''' =

Minimac3 uses maximum likelihood estimator for hard-call genotypes. For each haplotype, the allele with the maximum posterior probability is assigned, and the final genotype call is obtained from the hard-call haplotypes. For e.g. if the estimated posterior probability of the alternate allele is 0.56 and 0.60 in each haplotype, then the alternate allele is assigned to each haplotype and the final hard-call genotype is output as 1|1. Note that, the hard call genotype is NOT the MLE from the estimated genotype probabilities but instead from the estimated haplotype probabilities. For e.g. in this example, the posterior probability of the genotype 0|1 is maximum and equal to 0.48, but the output hard genotype is not 0|1 but 1|1, because at the haplotype level, each haplotype had more than 50% probability of alternate allele. As it is obvious, such cases will only arise when the sites are not imputed well.  

Minimac3 uses maximum likelihood estimator for hard-call genotypes. For each haplotype, the allele with the maximum posterior probability is assigned, and the final genotype call is obtained from the hard-call haplotypes. For e.g. if the estimated posterior probability of the alternate allele is 0.56 and 0.60 in each haplotype, then the alternate allele is assigned to each haplotype and the final hard-call genotype is output as 1|1. Note that, the hard call genotype is NOT the MLE from the estimated genotype probabilities but instead from the estimated haplotype probabilities. For e.g. in this example, the posterior probability of the genotype 0|1 is maximum and equal to 0.48, but the output hard genotype is not 0|1 but 1|1, because at the haplotype level, each haplotype had more than 50% probability of alternate allele. As it is obvious, such cases will only arise when the sites are not imputed well.  

= '''LooDosage''' =

= '''LooDosage''' =

Minimac3 uses an ad-hoc method to estimate imputation accuracy at sites that were genotyped in the study sample. For each such genotyped site, Minimac3 hides all known genotypes for that site and calculates an imputed dosage (in addition to the usual alternate allele dosage calculated assuming the genotypes are known at the site). This special imputed value is called Leave-One-Out dosage ('''LooDosage''') and is only available for genotyped sites. '''LooDosage''' is used to calculate Empirical-Rsquare ('''EmpR''', '''EmpRsq''') by directly calculating the Pearson correlation coefficient between '''LooDosage'''and known genotypes. It is also used to estimate the '''LooRsq'''.

Minimac3 uses an ad-hoc method to estimate imputation accuracy at sites that were genotyped in the study sample. For each such genotyped site, Minimac3 hides all known genotypes for that site and calculates an imputed dosage (in addition to the usual alternate allele dosage calculated assuming the genotypes are known at the site). This special imputed value is called Leave-One-Out dosage ('''LooDosage''') and is only available for genotyped sites. '''LooDosage''' is used to calculate Empirical-Rsquare ('''EmpR''', '''EmpRsq''') by directly calculating the Pearson correlation coefficient between '''LooDosage'''and known genotypes. It is also used to estimate the '''LooRsq'''.