RAREMETALWORKER command reference - Revision history

Abought at 21:47, 16 March 2018

2018-03-16T21:47:23Z

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			[[Category:RAREMETALWORKER]]
	==Useful Links==		==Useful Links==

Saichen at 16:22, 17 September 2015

2015-09-17T16:22:30Z

← Older revision		Revision as of 12:22, 17 September 2015
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	===--zip===		===--zip===
	* By issuing --zip, RAREMETALWORKER compress the [[ RAREMETALWORKER#Summary_Statistics\| '''summary statistics''']] and [[RAREMETALWORKER#LD_Matrices \| '''LD matrices''']] generated automatically, using gzip.		* By issuing --zip, RAREMETALWORKER compress the [[ RAREMETALWORKER#Summary_Statistics\| '''summary statistics''']] and [[RAREMETALWORKER#LD_Matrices \| '''LD matrices''']] generated automatically, using gzip. And the output zip files will be indexed using tabix.

	=== --thin ===		=== --thin ===

Shuang Feng: /* --geneMap */

2015-03-09T06:17:00Z

--geneMap

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	* --geneMap takes a string describing the path to find mapping file for manhattan plot annotation.		* --geneMap takes a string describing the path to find mapping file for manhattan plot annotation.
	* The default is human genome build 19, saved in raremetal/data/refFlat_hg19.txt.		* The default is human genome build 19, saved in raremetal/data/refFlat_hg19.txt.

			===--mergedVCFID===
			* This options allows RAREMETALWORKER to recognize VCF samples IDs in "FAMID_PID" format.
			* The default value is OFF, which means VCF sample IDs are consistent with PID field in PED file.

	==PhoneHome==		==PhoneHome==

Shuang Feng: /* --dosage */

2015-03-09T06:14:41Z

--dosage

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	* --dosage must be used with --vcf option.		* --dosage must be used with --vcf option.
	* Description of dosage format in a VCF file can be found in [[RAREMETALWORKER#DOSAGE \| '''dosage''']].		* Description of dosage format in a VCF file can be found in [[RAREMETALWORKER#DOSAGE \| '''dosage''']].

			===--flagDosage===
			* This option let user customize the name of field in VCF file that labels dosage data.
			* The default is "DS".

	===--noeof===		===--noeof===
	* If you VCF file does not have the BGZF EOF markers, you should use --noeof option to let RAREMETALWORKER skip checking the BGZF EOF markers at the end of the file.		* If you VCF file does not have the BGZF EOF markers, you should use --noeof option to let RAREMETALWORKER skip checking the BGZF EOF markers at the end of the file.

Shuang Feng: /* Useful Links */

2015-03-09T06:13:28Z

Useful Links

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	Options:		Options:
	Input Files : --ped [], --dat [], --vcf [], --dosage, --noeof		Input Files : --ped [], --dat [], --vcf [], --dosage, --flagDosage [DS],
			--noeof
	Output Files : --prefix [], --LDwindow [1000000], --zip, --thin,		Output Files : --prefix [], --LDwindow [1000000], --zip, --thin,
	--labelHits		--labelHits
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	--maleLabel [1], --femaleLabel [2]		--maleLabel [1], --femaleLabel [2]
	others : --cpu [1], --kinOnly,		others : --cpu [1], --kinOnly,
	--geneMap [../data/refFlat_hg19.txt]		--geneMap [../data/refFlat_hg19.txt], --mergedVCFID
	PhoneHome : --noPhoneHome, --phoneHomeThinning [100]		PhoneHome : --noPhoneHome, --phoneHomeThinning [100]

Shuang Feng: /* List of Options */

2014-06-19T16:08:09Z

List of Options

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	* The [[RAREMETAL_FAQ \| '''FAQ''']]		* The [[RAREMETAL_FAQ \| '''FAQ''']]

	~~==List of Options ==~~		Options:
			Input Files : --ped [], --dat [], --vcf [], --dosage, --noeof
	Options:		Output Files : --prefix [], --LDwindow [1000000], --zip, --thin,
	Input Files : --ped [], --dat [], --vcf [], --dosage, --noeof		--labelHits
	Output Files : --prefix [], --LDwindow [1000000], --zip, --thin,		VC Options : --vcX, --separateX
	--labelHits		Trait Options : --makeResiduals, --inverseNormal, --traitName []
	VC Options : --vcX, --separateX		Model Options : --recessive, --dominant
	Trait Options : --makeResiduals, --inverseNormal, --traitName []		Kinship Source : --kinPedigree, --kinGeno, --kinFile [], --kinxFile [],
	Model Options : --recessive, --dominant		--kinSave
	Kinship Source : --kinPedigree, --kinGeno, --kinFile [], --kinxFile [],		Kinship Options : --kinMaf [0.05], --kinMiss [0.05]
	--kinSave		Chromosome X : --xLabel [X], --xStart [2699520], --xEnd [154931044],
	Kinship Options : --kinMaf [0.05], --kinMiss [0.05]		--maleLabel [1], --femaleLabel [2]
	Chromosome X : --xLabel [X], --xStart [2699520], --xEnd [154931044],		others : --cpu [1], --kinOnly,
	--maleLabel [1], --femaleLabel [2]		--geneMap [../data/refFlat_hg19.txt]
	PhoneHome : --noPhoneHome, --phoneHomeThinning [100]		PhoneHome : --noPhoneHome, --phoneHomeThinning [100]

	==Input Files==		==Input Files==

Shuang Feng: /* Chromosome X */

2014-06-19T16:07:47Z

Chromosome X

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 * --xStart takes an integer that described the end position of nonPAR region on chromosome X.
 * The default is 154931044 based on Human Genome build 19.
 ==PhoneHome==

Shuang Feng: /* Useful Links */

2014-04-14T17:31:52Z

Useful Links

← Older revision		Revision as of 13:31, 14 April 2014
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	Here are some useful links to key pages:		Here are some useful links to key pages:
	* [[RAREMETALWORKER \| '''RAREMETALWORKER documentation''']]		* The [[RAREMETALWORKER \| '''RAREMETALWORKER documentation''']]
	* [[RAREMETALWORKER_METHOD \| '''RAREMETALWORKER method''']]		* The [[RAREMETALWORKER_METHOD \| '''RAREMETALWORKER method''']]
	* [[RAREMETALWORKER_SPECIAL_TOPICS \| '''RAREMETALWORKER special topics''']]		* The [[RAREMETALWORKER_SPECIAL_TOPICS \| '''RAREMETALWORKER special topics''']]
	* [[Tutorial:_RAREMETAL \| '''RAREMETALWORKER quick start tutorial''']]		* The [[Tutorial:_RAREMETAL \| '''RAREMETALWORKER quick start tutorial''']]
	* [[RAREMETAL_FAQ \| '''FAQ''']]		* The [[RAREMETAL_FAQ \| '''FAQ''']]

	==List of Options ==		==List of Options ==

Shuang Feng: /* Useful Links */

2014-04-14T17:30:13Z

Useful Links

← Older revision		Revision as of 13:30, 14 April 2014
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	* [[RAREMETALWORKER_METHOD \| '''RAREMETALWORKER method''']]		* [[RAREMETALWORKER_METHOD \| '''RAREMETALWORKER method''']]
	* [[RAREMETALWORKER_SPECIAL_TOPICS \| '''RAREMETALWORKER special topics''']]		* [[RAREMETALWORKER_SPECIAL_TOPICS \| '''RAREMETALWORKER special topics''']]
	* [[Tutorial:_RAREMETAL \| '''quick start tutorial''']]		* [[Tutorial:_RAREMETAL \| '''RAREMETALWORKER quick start tutorial''']]
	* [[RAREMETAL_FAQ \| '''FAQ''']]		* [[RAREMETAL_FAQ \| '''FAQ''']]

Shuang Feng: /* Useful Links */

2014-04-14T17:30:03Z

Useful Links

← Older revision		Revision as of 13:30, 14 April 2014
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	* [[RAREMETALWORKER_METHOD \| '''RAREMETALWORKER method''']]		* [[RAREMETALWORKER_METHOD \| '''RAREMETALWORKER method''']]
	* [[RAREMETALWORKER_SPECIAL_TOPICS \| '''RAREMETALWORKER special topics''']]		* [[RAREMETALWORKER_SPECIAL_TOPICS \| '''RAREMETALWORKER special topics''']]
	* [[Tutorial:_RAREMETAL \| ''quick start tutorial''']]		* [[Tutorial:_RAREMETAL \| '''quick start tutorial''']]
	* [[RAREMETAL_FAQ \| '''FAQ''']]		* [[RAREMETAL_FAQ \| '''FAQ''']]

← Older revision		Revision as of 13:31, 14 April 2014
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	Here are some useful links to key pages:		Here are some useful links to key pages:
	* [[RAREMETALWORKER \| '''RAREMETALWORKER documentation''']]		* The [[RAREMETALWORKER \| '''RAREMETALWORKER documentation''']]
	* [[RAREMETALWORKER_METHOD \| '''RAREMETALWORKER method''']]		* The [[RAREMETALWORKER_METHOD \| '''RAREMETALWORKER method''']]
	* [[RAREMETALWORKER_SPECIAL_TOPICS \| '''RAREMETALWORKER special topics''']]		* The [[RAREMETALWORKER_SPECIAL_TOPICS \| '''RAREMETALWORKER special topics''']]
	* [[Tutorial:_RAREMETAL \| '''RAREMETALWORKER quick start tutorial''']]		* The [[Tutorial:_RAREMETAL \| '''RAREMETALWORKER quick start tutorial''']]
	* [[RAREMETAL_FAQ \| '''FAQ''']]		* The [[RAREMETAL_FAQ \| '''FAQ''']]

	==List of Options ==		==List of Options ==

← Older revision		Revision as of 13:30, 14 April 2014
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	* [[RAREMETALWORKER_METHOD \| '''RAREMETALWORKER method''']]		* [[RAREMETALWORKER_METHOD \| '''RAREMETALWORKER method''']]
	* [[RAREMETALWORKER_SPECIAL_TOPICS \| '''RAREMETALWORKER special topics''']]		* [[RAREMETALWORKER_SPECIAL_TOPICS \| '''RAREMETALWORKER special topics''']]
	* [[Tutorial:_RAREMETAL \| '''quick start tutorial''']]		* [[Tutorial:_RAREMETAL \| '''RAREMETALWORKER quick start tutorial''']]
	* [[RAREMETAL_FAQ \| '''FAQ''']]		* [[RAREMETAL_FAQ \| '''FAQ''']]

← Older revision		Revision as of 13:30, 14 April 2014
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	* [[RAREMETALWORKER_METHOD \| '''RAREMETALWORKER method''']]		* [[RAREMETALWORKER_METHOD \| '''RAREMETALWORKER method''']]
	* [[RAREMETALWORKER_SPECIAL_TOPICS \| '''RAREMETALWORKER special topics''']]		* [[RAREMETALWORKER_SPECIAL_TOPICS \| '''RAREMETALWORKER special topics''']]
	* [[Tutorial:_RAREMETAL \| ''quick start tutorial''']]		* [[Tutorial:_RAREMETAL \| '''quick start tutorial''']]
	* [[RAREMETAL_FAQ \| '''FAQ''']]		* [[RAREMETAL_FAQ \| '''FAQ''']]