Tutorial: RAREMETAL - Revision history

Abought at 21:51, 16 March 2018

2018-03-16T21:51:58Z

← Older revision		Revision as of 17:51, 16 March 2018
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	[[Category:RAREMETAL]]		[[Category:RAREMETAL]]
	[[Category:~~RAREMETWALWORKER~~]]		[[Category:RAREMETALWORKER]]
	== Useful Wiki Pages ==		== Useful Wiki Pages ==

Abought at 21:51, 16 March 2018

2018-03-16T21:51:50Z

← Older revision		Revision as of 17:51, 16 March 2018
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			[[Category:RAREMETAL]]
			[[Category:RAREMETWALWORKER]]
	== Useful Wiki Pages ==		== Useful Wiki Pages ==

Goncalo: /* STEP 3: Run RAREMETAL for Meta-Analysis */

2014-01-29T20:48:54Z

STEP 3: Run RAREMETAL for Meta-Analysis

← Older revision		Revision as of 16:48, 29 January 2014
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	tabix -c "#" -s 1 -b 2 -e 2 STUDY2.QT1.singlevar.cov.txt.gz		tabix -c "#" -s 1 -b 2 -e 2 STUDY2.QT1.singlevar.cov.txt.gz

	* We next create two text files that will drive the meta-analysis. The first file lists the input files with summary statistics. Let's call it summaryfiles. In most Linux workstations, you can use the command pico or nano to create this file. These should be the contents of "summaryfiles":		* We next create two text files that will drive the meta-analysis. The first file lists the input files with summary statistics. Let's call it summaryfiles. In most Linux workstations, you can use the command pico or nano to create this file. These should be the contents of "summaryfiles":

	STUDY1.QT1.singlevar.score.txt.gz		STUDY1.QT1.singlevar.score.txt.gz

Goncalo: /* STEP 2: Analyze individual samples using RAREMETALWORKER */

2014-01-29T20:48:04Z

STEP 2: Analyze individual samples using RAREMETALWORKER

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	* We next analyse the second study using a similar command:		* We next analyse the second study using a similar command:

	raremetalworker --ped example2.ped --dat example2.dat --vcf example2.vcf.gz --traitName QT1		raremetalworker --ped example2.ped --dat example2.dat --vcf example2.vcf.gz --traitName QT1 \
	--inverseNormal --makeResiduals --kinSave --kinGeno --prefix STUDY2		--inverseNormal --makeResiduals --kinSave --kinGeno --prefix STUDY2

Goncalo: /* STEP 3: Run RAREMETAL for Meta-Analysis */

2014-01-29T20:47:41Z

STEP 3: Run RAREMETAL for Meta-Analysis

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	* Now, we are ready for meta-analysis. To perform single variant and gene-level meta-analyses all at once, use the following command:		* Now, we are ready for meta-analysis. To perform single variant and gene-level meta-analyses all at once, use the following command:

	raremetal --summaryFiles summaryfiles --covFiles covfiles --groupFile group.file --SKAT --burden --MB --VT		raremetal --summaryFiles summaryfiles --covFiles covfiles --groupFile group.file \
	~~--hwe 1.0e-05 --callRate 0.95~~ --longOutput --tabulateHits --hitsCutoff 1e-05 --prefix COMBINED.QT1		--SKAT --burden --MB --VT --longOutput --tabulateHits --hitsCutoff 1e-05 \
			--prefix COMBINED.QT1 --hwe 1.0e-05 --callRate 0.95 -

	This command filters summary statistics based on HWE p-value and variant call rate, generates single variant meta-analysis results, generates gene-level meta-analysis results using simple burden test, variable threshold test, Madson-Browning weighted burden test, and SKAT, tabulates significant genes with detailed single variant results included, and even generates some PDF files summarizing results.		This command filters summary statistics based on HWE p-value and variant call rate, generates single variant meta-analysis results, generates gene-level meta-analysis results using simple burden test, variable threshold test, Madson-Browning weighted burden test, and SKAT, tabulates significant genes with detailed single variant results included, and even generates some PDF files summarizing results.

Goncalo: /* STEP 2: Analyze individual samples using RAREMETALWORKER */

2014-01-29T20:44:43Z

STEP 2: Analyze individual samples using RAREMETALWORKER

← Older revision		Revision as of 16:44, 29 January 2014
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	* To analyse the first study, we execute the following command:		* To analyse the first study, we execute the following command:

	raremetalworker --ped example1.ped --dat example1.dat --vcf example1.vcf.gz --traitName QT1		raremetalworker --ped example1.ped --dat example1.dat --vcf example1.vcf.gz --traitName QT1 \
	--inverseNormal --makeResiduals --kinSave --kinGeno --prefix STUDY1		--inverseNormal --makeResiduals --kinSave --kinGeno --prefix STUDY1

Shuang Feng: /* STEP 2: Analyze individual samples using RAREMETALWORKER */

2014-01-29T15:16:13Z

STEP 2: Analyze individual samples using RAREMETALWORKER

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	--inverseNormal --makeResiduals --kinSave --kinGeno --prefix STUDY1		--inverseNormal --makeResiduals --kinSave --kinGeno --prefix STUDY1

	This command transforms phenotypes to normality (--inverseNormal), calculates trait residuals after adjusting for covariates (--makeResiduals), estimates relatedness between individuals and saves this for later use (--kinSave and --kinGeno), and even generates some ~~annotated~~ PDF files summarizing results ~~(--labelHits)~~.		This command transforms phenotypes to normality (--inverseNormal), calculates trait residuals after adjusting for covariates (--makeResiduals), estimates relatedness between individuals and saves this for later use (--kinSave and --kinGeno), and even generates some PDF files summarizing results.

	* After RAREMETALWORKER finishes running, you will see several output files:		* After RAREMETALWORKER finishes running, you will see several output files:

Shuang Feng: /* STEP 3: Run RAREMETAL for Meta-Analysis */

2014-01-29T15:15:28Z

STEP 3: Run RAREMETAL for Meta-Analysis

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	raremetal --summaryFiles summaryfiles --covFiles covfiles --groupFile group.file --SKAT --burden --MB --VT		raremetal --summaryFiles summaryfiles --covFiles covfiles --groupFile group.file --SKAT --burden --MB --VT
	--hwe 1.0e-05 --callRate 0.95 --longOutput --tabulateHits --hitsCutoff 1e-05 --prefix COMBINED.QT1 ~~--labelHits~~		--hwe 1.0e-05 --callRate 0.95 --longOutput --tabulateHits --hitsCutoff 1e-05 --prefix COMBINED.QT1

	This command filters summary statistics based on HWE p-value and variant call rate, generates single variant meta-analysis results, generates gene-level meta-analysis results using simple burden test, variable threshold test, Madson-Browning weighted burden test, and SKAT, tabulates significant genes with detailed single variant results included, and even generates some ~~annotated~~ PDF files summarizing results ~~(--labelHits)~~.		This command filters summary statistics based on HWE p-value and variant call rate, generates single variant meta-analysis results, generates gene-level meta-analysis results using simple burden test, variable threshold test, Madson-Browning weighted burden test, and SKAT, tabulates significant genes with detailed single variant results included, and even generates some PDF files summarizing results.

	* The following output will be generated:		* The following output will be generated:

Shuang Feng: /* STEP 3: Run RAREMETAL for Meta-Analysis */

2014-01-29T15:03:52Z

STEP 3: Run RAREMETAL for Meta-Analysis

← Older revision		Revision as of 11:03, 29 January 2014
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	--hwe 1.0e-05 --callRate 0.95 --longOutput --tabulateHits --hitsCutoff 1e-05 --prefix COMBINED.QT1 --labelHits		--hwe 1.0e-05 --callRate 0.95 --longOutput --tabulateHits --hitsCutoff 1e-05 --prefix COMBINED.QT1 --labelHits

	This command filters summary statistics based on HWE p-value and variant call rate, generates single variant meta-analysis results, generates gene-level meta-analysis results using simple burden test, variable threshold test, Madson-Browning weighted burden test, and SKAT, tabulates significant genes with detailed single variant results included, and it even ~~labels hits~~		This command filters summary statistics based on HWE p-value and variant call rate, generates single variant meta-analysis results, generates gene-level meta-analysis results using simple burden test, variable threshold test, Madson-Browning weighted burden test, and SKAT, tabulates significant genes with detailed single variant results included, and even generates some annotated PDF files summarizing results (--labelHits).

	* The following output will be generated:		* The following output will be generated:

Shuang Feng: /* STEP 3: Run RAREMETAL for Meta-Analysis */

2014-01-29T15:02:51Z

STEP 3: Run RAREMETAL for Meta-Analysis

← Older revision		Revision as of 11:02, 29 January 2014
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	--hwe 1.0e-05 --callRate 0.95 --longOutput --tabulateHits --hitsCutoff 1e-05 --prefix COMBINED.QT1 --labelHits		--hwe 1.0e-05 --callRate 0.95 --longOutput --tabulateHits --hitsCutoff 1e-05 --prefix COMBINED.QT1 --labelHits

			This command filters summary statistics based on HWE p-value and variant call rate, generates single variant meta-analysis results, generates gene-level meta-analysis results using simple burden test, variable threshold test, Madson-Browning weighted burden test, and SKAT, tabulates significant genes with detailed single variant results included, and it even labels hits

	* The following output will be generated:		* The following output will be generated: