RAREMETALWORKER - Revision history

Welchr: /* PED and DAT Files */

2019-11-20T17:34:13Z

PED and DAT Files

← Older revision		Revision as of 13:34, 20 November 2019
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	* '''Markers in PED and DAT file must be sorted by chromosome and position.'''		* '''Markers in PED and DAT file must be sorted by chromosome and position.'''

	* Covariate and trait values are saved in PED file. Covariate and trait descriptions are saved in DAT file.		* Covariate and trait values are saved in PED file. Covariate and trait descriptions are saved in DAT file. Note that you must specify <code>--makeResiduals</code> in order to adjust the covariates out of the phenotype. See [[RAREMETALWORKER#Example_Command_Lines \| Example Command Lines]] for examples and [[RAREMETALWORKER_command_reference#Trait_Options \| Trait Options]] for more information.

	==== VCF File ====		==== VCF File ====

2018-03-16T21:46:47Z

← Older revision		Revision as of 17:46, 16 March 2018
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			[[Category:RAREMETALWORKER]]

	'''RAREMETALWORKER''' is a tool for single variant analysis, generating summary statistics for gene level meta analyses in [http://genome.sph.umich.edu/wiki/RAREMETAL '''RAREMETAL'''].		'''RAREMETALWORKER''' is a tool for single variant analysis, generating summary statistics for gene level meta analyses in [http://genome.sph.umich.edu/wiki/RAREMETAL '''RAREMETAL'''].

2015-12-15T18:40:28Z

← Older revision		Revision as of 14:40, 15 December 2015
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	If you feel this program is useful, please tell us your name and contact in this [https://docs.google.com/spreadsheet/ccc?key=0AuYjznTeEDYudFpqUk9sQ2pkN3d3endjYldqMEp6ZUE&usp=sharing '''registration'''].		If you feel this program is useful, please tell us your name and contact in this [https://docs.google.com/spreadsheet/ccc?key=0AuYjznTeEDYudFpqUk9sQ2pkN3d3endjYldqMEp6ZUE&usp=sharing '''registration'''].

	If you have any questions, please contact Sai Chen (saichen at umich dot edu) or [[Goncalo_Abecasis \| '''Goncalo Abecasis''']] goncalo at umich dot edu.		If you have any questions, please contact Sai Chen (saichen at umich dot edu) or [[Goncalo_Abecasis \| '''Goncalo Abecasis''']] (goncalo at umich dot edu).

2015-12-15T18:40:15Z

← Older revision		Revision as of 14:40, 15 December 2015
Line 3:		Line 3:
	If you feel this program is useful, please tell us your name and contact in this [https://docs.google.com/spreadsheet/ccc?key=0AuYjznTeEDYudFpqUk9sQ2pkN3d3endjYldqMEp6ZUE&usp=sharing '''registration'''].		If you feel this program is useful, please tell us your name and contact in this [https://docs.google.com/spreadsheet/ccc?key=0AuYjznTeEDYudFpqUk9sQ2pkN3d3endjYldqMEp6ZUE&usp=sharing '''registration'''].

	If you have any questions, please contact [[Sai Chen ~~\|'''Sai Chen''']]~~ saichen at umich dot edu or [[Goncalo_Abecasis \| '''Goncalo Abecasis''']] goncalo at umich dot edu.		If you have any questions, please contact Sai Chen (saichen at umich dot edu) or [[Goncalo_Abecasis \| '''Goncalo Abecasis''']] goncalo at umich dot edu.

2015-12-15T18:39:40Z

← Older revision		Revision as of 14:39, 15 December 2015
Line 3:		Line 3:
	If you feel this program is useful, please tell us your name and contact in this [https://docs.google.com/spreadsheet/ccc?key=0AuYjznTeEDYudFpqUk9sQ2pkN3d3endjYldqMEp6ZUE&usp=sharing '''registration'''].		If you feel this program is useful, please tell us your name and contact in this [https://docs.google.com/spreadsheet/ccc?key=0AuYjznTeEDYudFpqUk9sQ2pkN3d3endjYldqMEp6ZUE&usp=sharing '''registration'''].

	If you have any questions, please contact [[Sai Chen\|'''Sai Chen''']] saichen at umich dot edu or [[Goncalo_Abecasis \| '''Goncalo Abecasis''']] goncalo at umich dot edu.		If you have any questions, please contact [[Sai Chen \|'''Sai Chen''']] saichen at umich dot edu or [[Goncalo_Abecasis \| '''Goncalo Abecasis''']] goncalo at umich dot edu.

2015-12-15T18:39:20Z

← Older revision		Revision as of 14:39, 15 December 2015
Line 3:		Line 3:
	If you feel this program is useful, please tell us your name and contact in this [https://docs.google.com/spreadsheet/ccc?key=0AuYjznTeEDYudFpqUk9sQ2pkN3d3endjYldqMEp6ZUE&usp=sharing '''registration'''].		If you feel this program is useful, please tell us your name and contact in this [https://docs.google.com/spreadsheet/ccc?key=0AuYjznTeEDYudFpqUk9sQ2pkN3d3endjYldqMEp6ZUE&usp=sharing '''registration'''].

	If you have any questions, please contact [[~~Shuang Feng~~\|'''~~Shuang Feng~~''']] ~~sfengsph~~ at umich dot edu or [[Goncalo_Abecasis \| '''Goncalo Abecasis''']] goncalo at umich dot edu.		If you have any questions, please contact [[Sai Chen\|'''Sai Chen''']] saichen at umich dot edu or [[Goncalo_Abecasis \| '''Goncalo Abecasis''']] goncalo at umich dot edu.

2015-12-14T00:55:28Z

Useful Wiki Pages

← Older revision		Revision as of 20:55, 13 December 2015
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	* The [[RAREMETAL_Documentation \| '''RAREMETAL documentation''']]		* The [[RAREMETAL_Documentation \| '''RAREMETAL documentation''']]
	* The [[RAREMETAL FAQ \| '''FAQ''']]		* The [[RAREMETAL FAQ \| '''FAQ''']]
	* The [[RAREMETAL_Change_Log \| "Change Log"]]		* The [[RAREMETAL_Change_Log \| '''Change Log''']]

	== Key Features ==		== Key Features ==

2015-12-14T00:55:14Z

Useful Wiki Pages

← Older revision		Revision as of 20:55, 13 December 2015
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	* The [[RAREMETAL_Documentation \| '''RAREMETAL documentation''']]		* The [[RAREMETAL_Documentation \| '''RAREMETAL documentation''']]
	* The [[RAREMETAL FAQ \| '''FAQ''']]		* The [[RAREMETAL FAQ \| '''FAQ''']]
			* The [[RAREMETAL_Change_Log \| "Change Log"]]

	== Key Features ==		== Key Features ==

2015-09-21T15:02:08Z

OUTPUT FILE NAMES

← Older revision		Revision as of 11:02, 21 September 2015
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	* If --zip option is used, then the following will be generated automatically:		* If --zip option is used, then the following will be generated automatically:
	prefix.traitName.singlevar.score.txt.gz		prefix.traitName.singlevar.score.txt.gz
			prefix.traitName.singlevar.score.txt.gz.tbi
	prefix.traitName.singlevar.cov.txt.gz		prefix.traitName.singlevar.cov.txt.gz
			prefix.traitName.singlevar.cov.txt.gz.tbi
	prefix.singlevar.log		prefix.singlevar.log

2015-05-17T18:28:14Z

LD Matrices

← Older revision		Revision as of 14:28, 17 May 2015
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	* prefix.traitName.singlevar.cov.txt contains the LD matrix among a variant and the adjacent markers within a prefixed-sized window. The default window size is 1MB. It has the following format:		* prefix.traitName.singlevar.cov.txt contains the LD matrix among a variant and the adjacent markers within a prefixed-sized window. The default window size is 1MB. It has the following format:

	CHR POS VAR_POS_IN_WINDOW LD_MATRIX		CHR POS VAR_POS_IN_WINDOW LD_MATRIX
	1 ~~762320~~ 762320,865628,865665,878744,879381,1560000 0.0359084,-0.000242112,-0.00125797,-0.000993422,-0.000344509,-0.00017077,		1 762320 762320,865628,865665,878744,879381,1560000 0.0359084,-0.000242112,-0.00125797,-0.000993422,-0.000344509,-0.00017077,
	1 865628 865628,865665,878744,879381,1560000,1864659 0.419804,-0.0103663,-0.00635265,0.0594056,0.0534505,-0.00462183,		1 865628 865628,865665,878744,879381,1560000,1864659 0.419804,-0.0103663,-0.00635265,0.0594056,0.0534505,-0.00462183,
	1 878744 878744,879381,1560000,1864659,1877659 0.000404537,-0.000235215,-1.4455e-05,-8.69137e-06,-3.1027e-05,		1 878744 878744,879381,1560000,1864659,1877659 0.000404537,-0.000235215,-1.4455e-05,-8.69137e-06,-3.1027e-05,

	=====Genomic Relationship Matrix (GRM)=====		=====Genomic Relationship Matrix (GRM)=====