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A typical Minimac3 command line would have the following parameter options:
Command Line Options:
Reference Haplotypes : --refHaps [], --passOnly
Target Haplotypes : --haps []
Output Parameters : --processReference, --prefix [Minimac3.Output],
--updateModel, --nobgzip, --doseOutput, --hapOutput,
--format [GT,DS]
Subset Parameters : --chr [], --start, --end, --window
Starting Parameters : --rec [], --err []
Estimation Parameters : --rounds [5], --states [200]
Other Parameters : --help, --cpus [1], --params
PhoneHome : --noPhoneHome, --phoneHomeThinning [50]
The most typically used parameter options are explained below with [[#Examples|examples]]. See subsection below for detailed [[#List of Options |list of available options]].
==Reference Haplotypes==
<font face=Courier>"--refHaps"</font> denotes the main input reference file could either be a VCF file or <font face=Courier>M3VCF</font> file. No handle is necessary for denoting type of file, program will detect it itself.
Minimac3 can handle both VCF files or <font face=Courier>M3VCF</font> files as input for the reference panel. The program can itself identify the type of file, and no handle is necessary for that. <font face=Courier>M3VCF</font> files are customized files created by Minimac3 (possibly in some previous run) that stores large reference panels in a compact form so as to save memory and computation time involved in reading large files. <font face=Courier>M3VCF</font> files must be generated in some previous run of Minimac3 and can be saved and used in later runs for faster loading of data. See section on [[#M3VCF Files| <font face=Courier>M3VCF</font>]] files and [[#Examples|examples]] below on how to use them.
==Target Haplotypes==
<font face=Courier>"--haps"</font> denotes the main input target file which has to be a VCF file (<font face=Courier>.vcf</font> or <font face=Courier>.vcf.gz</font>). The extensions are not mandatory.
Minimac3 can handle only VCF files as input for the target/gwas data. Note that input VCF files would be automatically assumed to be pre-phased. Markers which are in the target panel and NOT in the reference panel would be excluded from the output files. User must merge these extra markers back to the original data in order to analyze them. See [[#Examples|examples]] below.
==Output Files==
<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:
* '''DS''' : Estimated alternate allele dosage (default).
* '''GT''' : Estimated most likely genotype (default).
* '''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.
[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.]
