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<font face=Courier>"--prefix"</font> denotes the prefix for the output files (By default: <font face=Courier>Minimac3.Output</font>)
<font face=Courier>"--prefix"</font> denotes the prefix for the output files (By default: <font face=Courier>Minimac3.Output</font>)
Minimac3 can output files in both <font face=Courier>VCF</font> format and <font face=Courier>.dose</font> format (usual [http://genome.sph.umich.edu/wiki/Minimac minimac] output format). By default, Minimac3 will only output in <font face=Courier>VCF</font> format and users must use the handle <font face=Courier>--doseOutput</font> to output in <font face=Courier>.dose</font> format or the handle <font face=Courier>--hapOutput</font> 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 <font face=Courier>--format</font> (by default : <font face=Courier>--format DS,GT</font>) :
Minimac3 can output files in both <font face=Courier>VCF</font> format and <font face=Courier>.dose</font> format (usual [http://genome.sph.umich.edu/wiki/Minimac minimac] output format). By default, Minimac3 will only output in <font face=Courier>VCF</font> format and users must use the handle <font face=Courier>--doseOutput</font> to output in <font face=Courier>.dose</font> format or the handle <font face=Courier>--hapOutput</font> to output dosage data in phased format. Output VCF files can store dosage data only in the following formats and is managed by the handle <font face=Courier>--format</font> (by default : <font face=Courier>--format DS,GT</font>) :
* '''DS''' : Estimated alternate allele dosage (default).
* '''DS''' : Estimated alternate allele dosage (default).
