Changes

  Command Line Options:

  Command Line Options:

    Reference Haplotypes : --refHaps [], --passOnly

  Reference Haplotypes : --refHaps [], --passOnly, --rsid

       Target Haplotypes : --haps []

       Target Haplotypes : --haps []

       Output Parameters : --processReference, --prefix [Minimac3.Output],

       Output Parameters : --prefix [Minimac3.Output], --processReference,

                           --updateModel, --nobgzip, --doseOutput, --hapOutput,

                           --updateModel, --nobgzip, --vcfOutput [ON],

                          --format [GT,DS]

                          --doseOutput, --hapOutput, --format [GT,DS],

       Subset Parameters : --chr [], --start, --end, --window

       Subset Parameters : --chr [], --start, --end, --window

     Starting Parameters : --rec [], --err []

     Starting Parameters : --rec [], --err []

   Estimation Parameters : --rounds [5], --states [200]

   Estimation Parameters : --rounds [5], --states [200]

         Other Parameters : --help, --cpus [1], --params

         Other Parameters : --log, --lowMemory, --help, --cpus [1], --params

               PhoneHome : --noPhoneHome, --phoneHomeThinning [50]

               PhoneHome : --noPhoneHome, --phoneHomeThinning [50]

<font face=Courier>"--haps"</font> denotes the main input GWAS 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.  

<font face=Courier>"--haps"</font> denotes the main input GWAS 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.

Minimac3 can handle only VCF files as input for the GWAS data (see page on [[Minimac3 Cookbook : Converting Files to VCF|Converting Files to VCF]]). Note that input VCF files would be automatically assumed to be pre-phased (see page on [[Minimac3 Cookbook : Pre-Phasing|Pre-Phasing]]). 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.

==Output Files==

==Output Files==

[NOTE: While doing imputation, if parameter estimates are found in <font face=Courier>M3VCF</font> files, Minimac3 will automatically use them for imputation.  Users should use handle <font face=Courier>--updateModel</font> 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.]

[NOTE: While doing imputation, if parameter estimates are found in <font face=Courier>M3VCF</font> files, Minimac3 will automatically use them for imputation.  Users should use handle <font face=Courier>--updateModel</font> 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.]

== Subset Parameters ==

== Remaining Parameters ==

The subset parameters are required if the user wishes to

This sub-section explains the remaining parameters available.

== Starting Parameters ==

* '''Subset Parameters:''' The subset parameters are required if the user wishes to impute into a particular region of the chromosome rather than the whole chromosome (typically used when running imputation in chunks). For example, to analyze chromosome 6 from position 1000000 to position 2000000 with 500000 base positions on either side as a buffer, one must use <font face=Courier>--chr 6 --from 1000000  --to 2000000 --window 500000 </font>. If using the subset parameters, a default window of 500 Kbp is applied on either side, unless otherwise specified by the user. Variants from the buffer region are only used for imputation and not reported in the final output.

== Estimation Parameters ==

* '''Starting Parameters:''' The starting parameters are used if the users wishes to use some previously created parameter estimate files to save time on parameter estimation (<font face=Courier>.recom</font> and <font face=Courier>.erate</font> files can be used with <font face=Courier>--rec</font> and <font face=Courier>--err</font> respectively).

== Other Parameters ==

* '''Estimation Parameters:''' The estimation parameters specify the number of iterations (<font face=Courier>--rounds [5]</font>) and number of states (<font face=Courier>--states [200]</font>) to consider while implementing the Hidden Markov Model for parameter estimation. Default values of 5 and 200 are used (these would generally give accurate enough estimates and need not be increased unless the user has strong reasons to do so).

== PhoneHome ==

* '''Other Parameters:''' These parameters have varying usage. <font face=Courier>--help</font> would print out a brief documentation of Minimac3 and its usage, <font face=Courier>--cpus [5]</font> would allow the user to use multiple processors when running in parallel (this option is only available when running Minimac3-omp), <font face=Courier>--params</font> is used to print out the current values for the usage parameters,  <font face=Courier>--lowMemory</font> is used to run a lower memory version of Minimac3 that requires 33% lesser memory but 10% more time (for the HRC panel)

= Download =

= Download =

* [[Minimac3 Usage | Minimac3 Usage and Documentation]]

* [[Minimac3 Usage | Minimac3 Usage and Documentation]]

* [[Minimac3 Imputation Cookbook]] ('''Recommended for New Users!!''')

* [[Minimac3 Imputation Cookbook]] ('''Recommended for New Users!!''')

* [[Minimac3 Examples| Minimac3 Examples]]

* [[Minimac3 Examples| Minimac3 Examples]]