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== Chunking Parameters ==
== Chunking Parameters ==
Minimac4 automatically chunks the whole chromosome (into overlapping chunks), analyzes each chunk sequentially and then concatenates the imputed chunks back.
;--ChunkLengthMb <float_number>
: This option defines the average length of chunks in units of million base pairs (Mb). The input value should be within (0.001, 300]. The default setting is 20.
;--ChunkOverlapMb <float_number>
: This option defines the length of overlap between chunks in units of Mb, 3Mb by default. The valid input value should be within (0.001, 300].
: The overlap length should be at most 1/3 of the chunk length, if larger, Minimac4 will automatically reduce it to 1/3 of the chunk length.
== Subset Parameters ==
== Subset Parameters ==
This set of parameters are used when imputing a specific region instead of all the sites covered by the reference panel.
; --chr <chromosome>
: This option specifies the chromosome number for which we will carry out imputation.
: Note that it is required to specify non-zero values for <code>--start</code> and <code>--end</code> when <code>--chr</code> option is used.
; --start <integer>
: This option specifies the start position of the region to be analyzed. Would not work without <code>--chr</code> option.
; --end <integer>
: This option specifies the end position of the region to be analyzed. Would not work without <code>--chr</code> option.
; --window <integer>
: This option specifies the length of buffer region in units of base pairs on either side of the region to be analyzed. Would not work without <code>--chr</code> option; otherwise, it is set as 500000 by default.
== Approximation Parameters ==
== Approximation Parameters ==
;--minimac3
: OFF by default. If ON, Minimac3 algorithm will be used for imputation.
;--probThreshold <float_number>
;--diffThreshold <float_number>
;--topThreshold <float_number>
== Other Parameters ==
== Other Parameters ==
; --log
: OFF by default. If ON, information including warnings and errors will be saved into <output_prefix>.logfile, instead printed on the screen.
; --help
: If ON, it will show the list of all available options.
;--cpus <integer>
: This option defines the number of cpus for parallel computing, 1 by default.
== PhoneHome ==
== PhoneHome ==
;--noPhoneHome
: OFF by default. If ON, code will NOT send a SUCCESS/FAILURE status of the execution to home server.
;--phoneHomeThinning <integer>
: Percentage probability of sending SUCCESS/FAILURE status of the execution to home server, 50 by default.
