Minimac4 Documentation - Revision history

Yukt at 03:17, 20 July 2019

2019-07-20T03:17:05Z

← Older revision		Revision as of 23:17, 19 July 2019
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	;--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.



			[[Minimac4\| Back to Minimac4 Overview Page]]

Yukt: /* Subset Parameters */

2019-07-20T02:30:39Z

Subset Parameters

← Older revision		Revision as of 22:30, 19 July 2019
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	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.		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>.		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>

Yukt: /* PhoneHome */

2019-07-20T02:27:47Z

PhoneHome

← Older revision		Revision as of 22:27, 19 July 2019
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	== 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.

Yukt: /* Subset Parameters */

2019-07-20T02:25:42Z

Subset Parameters

← Older revision		Revision as of 22:25, 19 July 2019
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	== 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~~.		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>

Yukt: Almost done.

2019-07-20T02:15:52Z

Almost done.

@@ Line 75: / Line 75: @@
 == Chunking Parameters ==
 == Subset Parameters ==
 == Approximation Parameters ==
 ==  Other Parameters ==
 == PhoneHome ==

Yukt: Add output options

2019-07-17T00:50:33Z

Add output options

@@ Line 24: / Line 24: @@
 : If your reference panel is in VCF format, please use [[Minimac3]] to convert the VCF file to M3VCF (along with parameter estimation) and then use that M3VCF for imputation using Minimac4.
-;<s>--passOnly</s>
+; --passOnly
-: <s>DEACTIVATED! If ON, only variants will FILTER=PASS will be recorded from reference VCF file (does NOT work on M3VCF files yet).</s>
+:  DEACTIVATED for now. OFF by default. If ON, only variants will FILTER=PASS will be recorded from reference VCF file (does NOT work on M3VCF files yet).
 ;--rsid
-: If ON, Minimac4 will only import RS ID of variants from ID column of reference file (if available).
+: OFF by default. If ON, Minimac4 will only import RS ID of variants from ID column of reference file (if available).
 ;--referenceEstimates
@@ Line 36: / Line 36: @@
 : This option is automatically ignored except when <code>--referenceEstimates</code> is OFF.
 : It defines the genetic map file used for recombination rate estimation during imputation.
-: The input genetic map file should be tab-separated, with 1st column as chromosome id, 3rd column as cumulative recombination rate in cM/Mb, and 4th as genetic map coordinates in cM.
+: The input genetic map file should be tab-separated, with the first row as its header, and the columns representing chromosome id, base pair position, cumulative recombination rate in cM/Mb, and genetic map coordinates in cM, respectively.
 == Target Haplotypes ==
@@ Line 43: / Line 43: @@
 == Output Parameters ==
 == Chunking Parameters ==

Yukt: half done

2019-07-16T22:29:21Z

half done

New page

A typical Minimac4 command line would have the following parameter options:

Reference Haplotypes : --refHaps [], --passOnly, --rsid,
--referenceEstimates [ON],
--mapFile [docs/geneticMapFile.b38.map.txt.gz]
Target Haplotypes : --haps []
Output Parameters : --prefix [Minimac4.Output], --estimate,
--nobgzip, --vcfBuffer [200], --format [GT,DS],
--allTypedSites, --meta, --memUsage
Chunking Parameters : --ChunkLengthMb [20.00], --ChunkOverlapMb [3.00]
Subset Parameters : --chr [], --start, --end, --window
Approximation Parameters : --minimac3, --probThreshold [0.01],
--diffThreshold [0.01], --topThreshold [0.01]
Other Parameters : --log, --help, --cpus [1], --params
PhoneHome : --noPhoneHome, --phoneHomeThinning [50]

Among all, '''--refHaps''' and '''--haps''' are required.

== Reference Haplotypes ==
;--refHaps <input_m3vcf_filename>
: This option defines the reference panel in M3VCF format to impute against.
: If your reference panel is in VCF format, please use [[Minimac3]] to convert the VCF file to M3VCF (along with parameter estimation) and then use that M3VCF for imputation using Minimac4.

;<s>--passOnly</s>
: <s>DEACTIVATED! If ON, only variants will FILTER=PASS will be recorded from reference VCF file (does NOT work on M3VCF files yet).</s>

;--rsid
: If ON, Minimac4 will only import RS ID of variants from ID column of reference file (if available).

;--referenceEstimates
: ON by default. If ON, Minimac4 expects the input M3VCF file comes with parameter estimate; otherwise, a genetic map file for option <code>--mapFile</code> is required.

;--mapFile <input_genetic_map_file>
: This option is automatically ignored except when <code>--referenceEstimates</code> is OFF.
: It defines the genetic map file used for recombination rate estimation during imputation.
: The input genetic map file should be tab-separated, with 1st column as chromosome id, 3rd column as cumulative recombination rate in cM/Mb, and 4th as genetic map coordinates in cM.

== Target Haplotypes ==
;--haps <input_vcf_filename>
: This option defines the <u>pre-phased</u> target genotype data in VCF format to impute.

== Output Parameters ==

== Chunking Parameters ==

== Subset Parameters ==

== Approximation Parameters ==

== Other Parameters ==

== PhoneHome ==