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| − | = Full List of Options =
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| − | The following table gives a brief description of all the parameters of '''Minimac3'''. A detailed description would be available soon.
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| − | {| border="1" cellpadding="2"
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| − | |- bgcolor="lightgray"
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| − | ! scope="col" width="200px" | Parameter
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| − | ! scope="col" width="1225px" | Description
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| − | | <font face=Courier>--refHaps filename </font>
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| − | | VCF file or <font face=Courier>M3VCF</font> file containing haplotype data for reference panel.
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| − | |-
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| − | | <font face=Courier>--passOnly</font>
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| − | | If ON, only variants will FILTER=PASS will be recorded from reference VCF file (does NOT work on <font face=Courier>M3VCF</font> files yet).
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| − | |-
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| − | | <font face=Courier>--haps filename </font>
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| − | | File containing haplotype data for target (gwas) samples. Must be a VCF file.
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| − | |-
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| − | | <font face=Courier>--processReference</font>
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| − | | This option will only convert an input VCF file to M3VCF format (maybe for a later run of imputation). If this option is ON, no imputation would be performed and thus all other parameters will be ignored (of course, except for parameters on Reference Haplotypes and Subsetting Options). This option also does parameter estimation using the reference panel and saves them in the M3VCF file (the estimation can be skipped with <font face=Courier>rounds = 0</font>)
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| − | |-
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| − | | <font face=Courier>--prefix output </font>
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| − | | Prefix for all output files generated. By default: <font face=Courier>[Minimac3.Output]</font>
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| − | | <font face=Courier>--updateModel</font>
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| − | | If ON, saved parameter estimates read from a M3VCF file will be further updated using the gwas samples. Will be ignored if VCF reference file. [Default: OFF]
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| − | | <font face=Courier>--nobgzip</font>
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| − | | If ON, output files will be NOT bgzipped.
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| − | |-
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| − | | <font face=Courier>--doseOutput</font>
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| − | | If ON, imputed data will be output as dosage file as well [Default: OFF].
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| − | |-
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| − | | <font face=Courier>--hapOutput</font>
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| − | | If ON, phased imputed data will be output as well [Default: OFF].
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| − | |-
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| − | | <font face=Courier>--format</font>
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| − | | Specifies which fields to output for the FORMAT field in output VCF file. Available handles: <font face=Courier>GT,DS,GP </font>[Default: <font face=Courier>GT,DS</font>].
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| − | |-
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| − | | <font face=Courier>--chr 22</font>
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| − | | Chromosome number for which we will carry out imputation.
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| − | | <font face=Courier>--start 100000</font>
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| − | | Start position for imputation by chunking. Would not work without <font face=Courier>--chr</font> option.
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| − | | <font face=Courier>--end 200000</font>
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| − | | End position for imputation by chunking. Would not work without <font face=Courier>--chr</font> option.
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| − | | <font face=Courier>--window 5000</font>
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| − | | Length of buffer region on either side of <font face=Courier>--start</font> and <font face=Courier>--end</font>. By default = 0.
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| − | |-
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| − | | <font face=Courier>--rec</font>
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| − | | Recombination File from previous run of Minimac/Minimac3. (<font face=Courier>--err</font> parameter must also be provided, if using this handle)
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| − | |-
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| − | | <font face=Courier>--err</font>
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| − | | Error File from previous run of Minimac/Minimac3. (<font face=Courier>--rec</font> parameter must also be provided, if using this handle)
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| − | | <font face=Courier>--rounds 5</font>
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| − | | Rounds of optimization for model parameters, which describe population recombination rates and per SNP error rates. By default = 5.
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| − | | <font face=Courier>--states 200</font>
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| − | | Maximum number of reference (or target) haplotypes to be examined during parameter optimization. By default = 200.
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| − | | <font face=Courier>--help</font>
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| − | | A short help on options.
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| − | | <font face=Courier>--cpus 5</font>
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| − | | Number of cpus for parallel computing. Would work only with Minimac3-omp.
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| − | |-
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| − | | <font face=Courier>--noPhoneHome</font>
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| − | | If ON, code will NOT send a SUCCESS/FAILURE status of the execution to home server.
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| − | |-
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| − | | <font face=Courier>--phoneHomeThinning 50</font>
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| − | | Percentage probability of sending SUCCESS/FAILURE status of the execution to home server [Default: 50%]
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| − | |}
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| | = Download = | | = Download = |
