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, 22:55, 29 January 2015
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| This sub-section explains the remaining parameters available. | | This sub-section explains the remaining parameters available. |
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− | * Subset 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 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. |
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− | The subset parameters are required if the user wishes to | + | * '''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). |
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− | | + | * '''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). |
− | * Starting Parameters
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− | * Estimation Parameters | |
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| * Other Parameters | | * Other Parameters |
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− | * PhoneHome | + | * PhoneHome |
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| = Download = | | = Download = |