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== PhoneHome ==
== PhoneHome ==
= List of Options =
The following table gives a brief description of all the parameters of '''Minimac3'''. A detailed description would be available soon.
{| border="1" cellpadding="2"
|- bgcolor="lightgray"
! scope="col" width="200px" | Parameter
! scope="col" width="1225px" | Description
|-
| <code>--refHaps filename </code>
| VCF file or <code>M3VCF</code> file containing haplotype data for reference panel.
|-
| <code>--passOnly</code>
| If ON, only variants will FILTER=PASS will be recorded from reference VCF file (does NOT work on <code>M3VCF</code> files yet).
|-
| <code>--haps filename </code>
| File containing haplotype data for target (gwas) samples. Must be a VCF file.
|-
| <code>--processReference</code>
| 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 <code>rounds = 0</code>)
|-
| <code>--prefix output </code>
| Prefix for all output files generated. By default: <code>[Minimac3.Output]</code>
|-
| <code>--updateModel</code>
| 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]
|-
| <code>--nobgzip</code>
| If ON, output files will be NOT bgzipped.
|-
| <code>--doseOutput</code>
| If ON, imputed data will be output as dosage file as well [Default: OFF].
|-
| <code>--hapOutput</code>
| If ON, phased imputed data will be output as well [Default: OFF].
|-
| <code>--format</code>
| Specifies which fields to output for the FORMAT field in output VCF file. Available handles: <code>GT,DS,GP </code>[Default: <code>GT,DS</code>].
|-
| <code>--chr 22</code>
| Chromosome number for which we will carry out imputation.
|-
| <code>--start 100000</code>
| Start position for imputation by chunking. Would not work without <code>--chr</code> option.
|-
| <code>--end 200000</code>
| End position for imputation by chunking. Would not work without <code>--chr</code> option.
|-
| <code>--window 5000</code>
| Length of buffer region on either side of <code>--start</code> and <code>--end</code>. By default = 0.
|-
| <code>--rec</code>
| Recombination File from previous run of Minimac/Minimac3. (<code>--err</code> parameter must also be provided, if using this handle)
|-
| <code>--err</code>
| Error File from previous run of Minimac/Minimac3. (<code>--rec</code> parameter must also be provided, if using this handle)
|-
| <code>--rounds 5</code>
| Rounds of optimization for model parameters, which describe population recombination rates and per SNP error rates. By default = 5.
|-
| <code>--states 200</code>
| Maximum number of reference (or target) haplotypes to be examined during parameter optimization. By default = 200.
|-
| <code>--help</code>
| A short help on options.
|-
| <code>--cpus 5</code>
| Number of cpus for parallel computing. Would work only with Minimac3-omp.
|-
| <code>--noPhoneHome</code>
| If ON, code will NOT send a SUCCESS/FAILURE status of the execution to home server.
|-
| <code>--phoneHomeThinning 50</code>
| Percentage probability of sending SUCCESS/FAILURE status of the execution to home server [Default: 50%]
|}
= Download =
= Download =
