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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 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.
* '''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.
* '''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).
* '''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).
