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, 00:35, 29 January 2015
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| = Detailed Usage = | | = Detailed Usage = |
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− | 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]]. | + | The available options of Minimac3 are explained in detail below. See wiki page on [[Minimac3 Examples|Examples]] and subsection below for [[#List of Options |full list of available options]]. |
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| ==Reference Haplotypes== | | ==Reference Haplotypes== |
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− | <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. | + | <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. |
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− | 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. | + | 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 wiki page on[[M3VCF Files| <font face=Courier>M3VCF</font> files]] and [[Minimac3 Examples|Examples]] on how to use them. |
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| ==Target Haplotypes== | | ==Target Haplotypes== |