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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 ==
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>
: 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 ==
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
: 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.
[[Minimac4| Back to Minimac4 Overview Page]]
