Minimac Diagnostics

minimac is a tool for imputation of missing genotypes into phased haplotypes. At the end of each run, minimac generates summaries of imputation quality and stores those in a .info file.

Basic Descriptors

The first three columns in the .info file list marker name and alleles for each marker. Typically, the most common allele will be listed first, but this is not guaranteed.

The next column in the .info file lists the estimated frequency of allele 1 - this corresponds to the average number of imputed copies of allele 1 for each individual, divided by two.

Frequency information is followed by an estimate of the squared correlation between imputed genotypes and true, unobserved genotypes. Since true genotypes are not available, this calculation is based on the idea that poorly imputed genotype counts will shrink towards their expectations based on population allele frequencies alone; specifically $2p$ where $p$ is the frequency of the allele being imputed.

Currently, minimac uses the following definition:

${\hat {r}}^{2}={{Var({\mbox{Estimated Counts}})} \over {{\hat {p}}(1-{\hat {p}})}}$