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= Detailed Usage =
= Detailed Usage =
The most typically used parameter options are explained below. See wiki page on [[Minimac3 Examples|Examples]] and subsection below for detailed [[#List of Options |list of available options]].
The available options of Minimac3 are explained in detail below. See wiki page on [[Minimac3 Examples|Examples]] and subsection below for full [[#List of Options |list of available options]].
==Reference Haplotypes==
==Reference Haplotypes==
[NOTE: If parameter estimates are found in <code>M3VCF</code> files, Minimac3 will automatically use them for imputation. Users should use handle <code>--updateModel</code> in order to update the parameter estimates using the target/gwas panel as well. However, this is NOT necessary in most cases, unless the user has strong reasons to believe that this might increase the imputation accuracy.]
[NOTE: If parameter estimates are found in <code>M3VCF</code> files, Minimac3 will automatically use them for imputation. Users should use handle <code>--updateModel</code> in order to update the parameter estimates using the target/gwas panel as well. However, this is NOT necessary in most cases, unless the user has strong reasons to believe that this might increase the imputation accuracy.]
= Download =
= Download =
