Minimac3 Usage - Revision history

Santy.8128: /* Remaining Parameters */

2016-06-06T23:32:10Z

Remaining Parameters

← Older revision		Revision as of 19:32, 6 June 2016
Line 63:		Line 63:
	* '''Estimation Parameters:''' The estimation parameters specify the number of iterations (<font face=Courier>--rounds [5]</font>) and number of states (<font face=Courier>--states [200]</font>) to consider while implementing the Hidden Markov Model for parameter estimation. Default values of 5 and 200 are used (these would generally give accurate enough estimates and need not be increased unless the user has strong reasons to do so).		* '''Estimation Parameters:''' The estimation parameters specify the number of iterations (<font face=Courier>--rounds [5]</font>) and number of states (<font face=Courier>--states [200]</font>) to consider while implementing the Hidden Markov Model for parameter estimation. Default values of 5 and 200 are used (these would generally give accurate enough estimates and need not be increased unless the user has strong reasons to do so).

	* '''Other Parameters:''' These parameters have varying usage. <font face=Courier>--help</font> would print out a brief documentation of Minimac3 and its usage, <font face=Courier>--cpus [5]</font> would allow the user to use multiple processors when running in parallel (this option is only available when running Minimac3-omp), <font face=Courier>--params</font> is used to print out the current values for the usage parameters.		* '''Other Parameters:''' These parameters have varying usage. <font face=Courier>--help</font> would print out a brief documentation of Minimac3 and its usage, <font face=Courier>--cpus [5]</font> would allow the user to use multiple processors when running in parallel (this option is only available when running Minimac3-omp), <font face=Courier>--params</font> is used to print out the current values for the usage parameters, <font face=Courier>--lowMemory</font> is used to run a lower memory version of Minimac3 that requires 33% lesser memory but 10% more time (for the HRC panel)

	* '''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 <font face=Courier>--noPhoneHome</font> to opt out from this option or should use <font face=Courier>--phoneHomeThinning 50</font> to send back a message with 50% chance (typically used when running lots of command lines).		* '''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 <font face=Courier>--noPhoneHome</font> to opt out from this option or should use <font face=Courier>--phoneHomeThinning 50</font> to send back a message with 50% chance (typically used when running lots of command lines).

Santy.8128: /* Command Line Options */

2016-06-06T23:31:02Z

Command Line Options

← Older revision		Revision as of 19:31, 6 June 2016
Line 11:		Line 11:

	Command Line Options:		Command Line Options:
	Reference Haplotypes : --refHaps [], --passOnly, --rsid		Reference Haplotypes : --refHaps [], --passOnly, --rsid
	Target Haplotypes : --haps []		Target Haplotypes : --haps []
	Output Parameters : --prefix [Minimac3.Output], --processReference,		Output Parameters : --prefix [Minimac3.Output], --processReference,
Line 20:		Line 20:
	Starting Parameters : --rec [], --err []		Starting Parameters : --rec [], --err []
	Estimation Parameters : --rounds [5], --states [200]		Estimation Parameters : --rounds [5], --states [200]
	Other Parameters : --log, --help, --cpus [1], --params		Other Parameters : --log, --lowMemory, --help, --cpus [1], --params
	PhoneHome : --noPhoneHome, --phoneHomeThinning [50]		PhoneHome : --noPhoneHome, --phoneHomeThinning [50]

Santy.8128: /* Remaining Parameters */

2016-05-20T15:31:41Z

Remaining Parameters

← Older revision		Revision as of 11:31, 20 May 2016
Line 57:		Line 57:
	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).

Santy.8128: /* Command Line Options */

2015-10-18T01:52:04Z

Command Line Options

← Older revision		Revision as of 21:52, 17 October 2015
Line 11:		Line 11:

	Command Line Options:		Command Line Options:
	Reference Haplotypes : --refHaps [], --passOnly		Reference Haplotypes : --refHaps [], --passOnly, --rsid
	Target Haplotypes : --haps []		Target Haplotypes : --haps []
	Output Parameters : ~~--processReference,~~ --prefix [Minimac3.Output],		Output Parameters : --prefix [Minimac3.Output], --processReference,
	--updateModel, --nobgzip, --doseOutput, --hapOutput,		--updateModel, --nobgzip, --vcfOutput [ON],
	--format [GT,DS]		--doseOutput, --hapOutput, --format [GT,DS],
			--allTypedSites
	Subset Parameters : --chr [], --start, --end, --window		Subset Parameters : --chr [], --start, --end, --window
	Starting Parameters : --rec [], --err []		Starting Parameters : --rec [], --err []
	Estimation Parameters : --rounds [5], --states [200]		Estimation Parameters : --rounds [5], --states [200]
	Other Parameters : --help, --cpus [1], --params		Other Parameters : --log, --help, --cpus [1], --params
	PhoneHome : --noPhoneHome, --phoneHomeThinning [50]		PhoneHome : --noPhoneHome, --phoneHomeThinning [50]

Santy.8128: /* Useful Wiki Pages */

2015-01-30T03:24:31Z

Useful Wiki Pages

← Older revision		Revision as of 23:24, 29 January 2015
Line 81:		Line 81:

	* [[Minimac3 Imputation Cookbook]] ('''Recommended for New Users!!''')		* [[Minimac3 Imputation Cookbook]] ('''Recommended for New Users!!''')

			* [[Minimac3 Cookbook : Pre-Phasing \| Pre-Phasing ]]

			* [[Minimac3 Cookbook : Converting Files to VCF\| Converting Files to VCF]]

	* [[Minimac3 Examples\| Minimac3 Examples]]		* [[Minimac3 Examples\| Minimac3 Examples]]

Santy.8128: /* Target Haplotypes */

2015-01-30T03:23:07Z

Target Haplotypes

← Older revision		Revision as of 23:23, 29 January 2015
Line 36:		Line 36:
	<font face=Courier>"--haps"</font> denotes the main input GWAS file which has to be a VCF file (<font face=Courier>.vcf</font> or <font face=Courier>.vcf.gz</font>). The extensions are not mandatory.		<font face=Courier>"--haps"</font> denotes the main input GWAS file which has to be a VCF file (<font face=Courier>.vcf</font> or <font face=Courier>.vcf.gz</font>). The extensions are not mandatory.

	Minimac3 can handle only VCF files as input for the ~~target/gwas~~ data. Note that input VCF files would be automatically assumed to be pre-phased. Markers which are in the target panel and NOT in the reference panel would be excluded from the output files. User must merge these extra markers back to the original data in order to analyze them.		Minimac3 can handle only VCF files as input for the GWAS data (see page on [[Minimac3 Cookbook : Converting Files to VCF\|Converting Files to VCF]]). Note that input VCF files would be automatically assumed to be pre-phased (see page on [[Minimac3 Cookbook : Pre-Phasing\|Pre-Phasing]]). Markers which are in the target panel and NOT in the reference panel would be excluded from the output files. User must merge these extra markers back to the original data in order to analyze them.

	==Output Files==		==Output Files==

Santy.8128: /* Useful Wiki Pages */

2015-01-30T03:20:24Z

Useful Wiki Pages

← Older revision		Revision as of 23:20, 29 January 2015
Line 77:		Line 77:

	* [[Minimac3 Usage \| Minimac3 Usage and Documentation]]		* [[Minimac3 Usage \| Minimac3 Usage and Documentation]]

			* [[Minimac3 - Full List of Options]]

	* [[Minimac3 Imputation Cookbook]] ('''Recommended for New Users!!''')		* [[Minimac3 Imputation Cookbook]] ('''Recommended for New Users!!''')

Santy.8128: /* Remaining Parameters */

2015-01-30T03:06:35Z

Remaining Parameters

← Older revision		Revision as of 23:06, 29 January 2015
Line 64:		Line 64:
	* '''Other Parameters:''' These parameters have varying usage. <font face=Courier>--help</font> would print out a brief documentation of Minimac3 and its usage, <font face=Courier>--cpus [5]</font> would allow the user to use multiple processors when running in parallel (this option is only available when running Minimac3-omp), <font face=Courier>--params</font> is used to print out the current values for the usage parameters.		* '''Other Parameters:''' These parameters have varying usage. <font face=Courier>--help</font> would print out a brief documentation of Minimac3 and its usage, <font face=Courier>--cpus [5]</font> would allow the user to use multiple processors when running in parallel (this option is only available when running Minimac3-omp), <font face=Courier>--params</font> is used to print out the current values for the usage parameters.

	* '''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.		* '''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 <font face=Courier>--noPhoneHome</font> to opt out from this option or should use <font face=Courier>--phoneHomeThinning 50</font> to send back a message with 50% chance (typically used when running lots of command lines).

	= Download =		= Download =

Santy.8128: /* Remaining Parameters */

2015-01-30T03:02:13Z

Remaining Parameters

← Older revision		Revision as of 23:02, 29 January 2015
Line 56:		Line 56:
	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, 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 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.

	* '''Starting Parameters:''' The starting parameters are used if the users wishes to use some previously created parameter estimate files (<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).

	* '''Estimation Parameters:''' The estimation parameters specify the number of iterations (<font face=Courier>--rounds [5]</font>) and number of states (<font face=Courier>--states [200]</font>) to consider while implementing the Hidden Markov Model for parameter estimation. Default values of 5 and 200 are used (these would generally give accurate enough estimates and need not be increased unless the user has strong reasons to do so).		* '''Estimation Parameters:''' The estimation parameters specify the number of iterations (<font face=Courier>--rounds [5]</font>) and number of states (<font face=Courier>--states [200]</font>) to consider while implementing the Hidden Markov Model for parameter estimation. Default values of 5 and 200 are used (these would generally give accurate enough estimates and need not be increased unless the user has strong reasons to do so).

	* Other Parameters		* '''Other Parameters:''' These parameters have varying usage. <font face=Courier>--help</font> would print out a brief documentation of Minimac3 and its usage, <font face=Courier>--cpus [5]</font> would allow the user to use multiple processors when running in parallel (this option is only available when running Minimac3-omp), <font face=Courier>--params</font> is used to print out the current values for the usage parameters.

	* 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.

	= Download =		= Download =

Santy.8128: /* Remaining Parameters */

2015-01-30T02:55:21Z

Remaining Parameters

← Older revision		Revision as of 22:55, 29 January 2015
Line 56:		Line 56:
	This sub-section explains the remaining parameters available.		This sub-section explains the remaining parameters available.

	* 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). 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, 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		* '''Starting Parameters:''' The starting parameters are used if the users wishes to use some previously created parameter estimate files (<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).

			* '''Estimation Parameters:''' The estimation parameters specify the number of iterations (<font face=Courier>--rounds [5]</font>) and number of states (<font face=Courier>--states [200]</font>) to consider while implementing the Hidden Markov Model for parameter estimation. Default values of 5 and 200 are used (these would generally give accurate enough estimates and need not be increased unless the user has strong reasons to do so).
	* Starting Parameters

	* Estimation Parameters

	* Other Parameters		* Other Parameters

	* PhoneHome		* PhoneHome


	= Download =		= Download =