Minimac3 is a low memory and computationally efficient implementation of the genotype imputation algorithms. Minimac3 is designed to handle very large reference panels in a more computationally efficient way with no loss of accuracy.
Thanks for noticing this. I merged the changes. We will release minimac4 in a couple of weeks, so haven't been paying much attention to minimac3. Thanks though.
Added new line output for line 428 since ifprintf(vcfdosepartial,"##FILTER="); was causing the lines to blend together.