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==Reference Haplotypes==
==Reference Haplotypes==
Minimac3 can handle either 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 below on how to use them.
Minimac3 can handle either 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.
<font face=Courier>"--refHaps"</font> denotes the main input reference file which is either a VCF file or <font face=Courier>M3VCF</font> file. No handle is necessary for denoting type of file, program will detect it itself.
<font face=Courier>"--refHaps"</font> denotes the main input reference file which is either 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 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.
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.
<font face=Courier>"--haps"</font> denotes the main input target file which is a VCF file (<font face=Courier>.vcf</font> or <font face=Courier>.vcf.gz</font>). The extensions are not mandatory. See examples below.
<font face=Courier>"--haps"</font> denotes the main input target file which is a VCF file (<font face=Courier>.vcf</font> or <font face=Courier>.vcf.gz</font>). The extensions are not mandatory. See [[#Examples|examples]] below.
==Output Files==
==Output Files==
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>).
See [[#Examples|examples]] and the [[#List of Options|list of options]] below for further details.
= Examples =
= Examples =
