Changes

<font face=Courier>"--prefix"</font> denotes the prefix for the output files (By default: <code>Minimac3.Output</code>)

<font face=Courier>"--prefix"</font> denotes the prefix for the output files (By default: <code>Minimac3.Output</code>)

Minimac3 can output files in both <code>VCF</code> format and <code>.dose</code> format (usual [http://genome.sph.umich.edu/wiki/Minimac minimac] output format). By default, Minimac3 will only output in <code>VCF</code> format and users must use the handle <code>--doseOutput</code> to output in <code>.dose</code> format or the handle <code>--hapOutput</code> to output dosage data in phased format. VCF files can store dosage data only in the following formats:

Minimac3 can output files in both <code>VCF</code> format and <code>.dose</code> format (usual [http://genome.sph.umich.edu/wiki/Minimac minimac] output format). By default, Minimac3 will only output in <code>VCF</code> format and users must use the handle <code>--doseOutput</code> to output in <code>.dose</code> format or the handle <code>--hapOutput</code> to output dosage data in phased format. Output VCF files can store dosage data only in the following formats and in managed by the handle <code>--format</code> (by default : <code>--format DS,GT</code>) :

* '''DS''' : Estimated alternate allele dosage (default).

* '''DS''' : Estimated alternate allele dosage (default).

* '''GP''' : Estimated posterior genotype probabilities (use handle <code>--format GP</code>).

* '''GP''' : Estimated posterior genotype probabilities (use handle <code>--format GP</code>).

The handle <code>--processReference</code> is used to ONLY convert reference panels from <code>VCF</code> format to [[#M3VCF Files|<font face=Courier>M3VCF</font>]] format (and save parameter estimates). NO imputation will be performed and thus NO target/gwas haplotypes are required. However, by default, parameter estimation will be done using the reference panel and the estimates will be saved in the <code>M3VCF</code> files. Users should use <code>--rounds  0</code> in order to opt out of parameter estimation and only compress the reference panel and save it as a <code>M3VCF</code> file. See [[#Examples|examples]] and the [[#List of Options|list of options]] below for further details.

The handle <code>--processReference</code> is used to ONLY convert reference panels from <code>VCF</code> format to [[M3VCF Files|<font face=Courier>M3VCF</font>]] format (and save parameter estimates). NO imputation will be performed and thus NO target/gwas haplotypes are required. However, by default, parameter estimation will be done using the reference panel and the estimates will be saved in the <code>M3VCF</code> files. Users should use <code>--rounds  0</code> in order to opt out of parameter estimation and only compress the reference panel and save it as a <code>M3VCF</code> file. See wiki page on [[Minimac3 Examples|Examples]] for further details.

[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: While doing imputation, 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 =

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