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=== '''Does --mle overwrite fed-in genotypes?''' ===

=== Does --mle overwrite input genotypes?  ===

A: Yes. But rarely. --mle outputs the most likely genotype guesses by integrating over the probabilities of all possible configurations based on the reference haplotypes. The overwriting happens when the most likely guess differs from the experimental counterpart.<br><br>

A: Yes, but not often. The --mle option outputs the most likely genotype configuration taking into account observed genotypes and integration over the most similar reference haplotypes. The original genotypes will be changed only if the underlying reference haplotypes strongly contradict the input genotype.

=== '''How do I get imputation quality estimates?'''  ===

=== '''How do I get imputation quality estimates?'''  ===