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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). If using the subset parameters, a default window of additional 500 Kbp is applied on either side as the buffer region, unless otherwise specified by the user. Variants from the buffer region are only used for imputation and not reported in the final output.
For example, to analyze chromosome 6 from position 1000000 to position 2000000 with 300000 base positions on either side as a buffer, one must use <code>--chr 6 --from 1000000 --to 2000000 --window 300000</code>.
; --chr <chromosome>
; --chr <chromosome>
== 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. User should use the handle <code>--noPhoneHome</code> to opt out from this option or should use <code>--phoneHomeThinning 50</code> to send back a message with 50% chance (typically used when running lots of command lines).
;--noPhoneHome
;--noPhoneHome
: OFF by default. If ON, code will NOT send a SUCCESS/FAILURE status of the execution to home server.
: OFF by default. If ON, code will NOT send a SUCCESS/FAILURE status of the execution to home server.
;--phoneHomeThinning <integer>
;--phoneHomeThinning <integer>
: Percentage probability of sending SUCCESS/FAILURE status of the execution to home server, 50 by default.
: Percentage probability of sending SUCCESS/FAILURE status of the execution to home server, 50 by default.
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