Changes

This sub-section explains the remaining parameters available.

This sub-section explains the remaining parameters available.

* '''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 1Mbp is applied, unless otherwise specified by the user. Variants from the buffer region are only used for imputation and not reported in the final output.

* '''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 1Mbp 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.

* '''Starting Parameters:''' The starting parameters are used if the users wishes to use some previously created parameter estimate files (<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).

* '''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).

* '''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

* '''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.

* PhoneHome

* '''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.

= Download =

= Download =