Changes

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

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

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.

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?'''  ===