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Command Line Options:
Command Line Options:
Reference Haplotypes : --refHaps [], --passOnly, --rsid
Target Haplotypes : --haps []
Target Haplotypes : --haps []
Output Parameters : --prefix [Minimac3.Output], --processReference,
Output Parameters : --prefix [Minimac3.Output], --processReference,
Starting Parameters : --rec [], --err []
Starting Parameters : --rec [], --err []
Estimation Parameters : --rounds [5], --states [200]
Estimation Parameters : --rounds [5], --states [200]
Other Parameters : --log, --help, --cpus [1], --params
Other Parameters : --log, --lowMemory, --help, --cpus [1], --params
PhoneHome : --noPhoneHome, --phoneHomeThinning [50]
PhoneHome : --noPhoneHome, --phoneHomeThinning [50]
* '''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).
* '''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).
* '''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.
* '''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)
* '''PhoneHome:''' This option (by default) sends a message to a University of Michigan database about the success/failure of the analysis run (and as to what kind of failure had occurred, if so). No information about the data, file or file-name is sent back. User should use the handle <font face=Courier>--noPhoneHome</font> to opt out from this option or should use <font face=Courier>--phoneHomeThinning 50</font> to send back a message with 50% chance (typically used when running lots of command lines).
* '''PhoneHome:''' This option (by default) sends a message to a University of Michigan database about the success/failure of the analysis run (and as to what kind of failure had occurred, if so). No information about the data, file or file-name is sent back. User should use the handle <font face=Courier>--noPhoneHome</font> to opt out from this option or should use <font face=Courier>--phoneHomeThinning 50</font> to send back a message with 50% chance (typically used when running lots of command lines).
