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| * The [[RAREMETALWORKER|RAREMETALWORKER documentation]] | | * The [[RAREMETALWORKER|RAREMETALWORKER documentation]] |
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| + | * The [http://genome.sph.umich.edu/wiki/Rvtests '''rvtests'''] |
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| == Key Features == | | == Key Features == |
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| == Brief Description == | | == Brief Description == |
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− | '''RAREMETAL''' is a computationally efficient tool for meta-analysis of rare variants using sequencing or genotyping array data. '''RAREMETAL''' takes summary statistics and LD matrices generated by [[Rare-Metal-Worker|'''RAREMETALWORKER''']], handles related and unrelated individuals, and supports both single variant and burden meta-analysis. '''RAREMETAL''' generated high quality plots by default and has options that allow users to build reports at different levels. | + | '''RAREMETAL''' is a computationally efficient tool for meta-analysis of rare variants using sequencing or genotyping array data. '''RAREMETAL''' takes summary statistics and LD matrices generated by [[Rare-Metal-Worker|'''RAREMETALWORKER''']] or [http://genome.sph.umich.edu/wiki/Rvtests '''rvtests'''], handles related and unrelated individuals, and supports both single variant and burden meta-analysis. '''RAREMETAL''' generated high quality plots by default and has options that allow users to build reports at different levels. |
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| '''RAREMETAL''' is developed by Shuang Feng, Dajiang Liu and Gonçalo Abecasis. A R-package using the same methodology is [[RareMetals|available]]]. Manuscript for this tool is in preparation. Please contact sfengsph at umich dot edu for questions. | | '''RAREMETAL''' is developed by Shuang Feng, Dajiang Liu and Gonçalo Abecasis. A R-package using the same methodology is [[RareMetals|available]]]. Manuscript for this tool is in preparation. Please contact sfengsph at umich dot edu for questions. |
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| ==== Prepare Input Files==== | | ==== Prepare Input Files==== |
− | '''rareMETAL''' requires the following basic input files: summary statistics and covariance matrices of score statistics generated by '''rareMetalWorker''', a file with list of studies to be included and a group file if gene-level meta-analysis is expected. | + | '''rareMETAL''' requires the following basic input files: summary statistics and covariance matrices of score statistics generated by '''rareMetalWorker''' or [http://genome.sph.umich.edu/wiki/Rvtests '''rvtests'''], a file with list of studies to be included and a group file if gene-level meta-analysis is expected. |
| + | or [http://genome.sph.umich.edu/wiki/Rvtests '''rvtests'''] |
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| =====Summary Statistics===== | | =====Summary Statistics===== |
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| bgzip study1.singlevar.cov.txt | | bgzip study1.singlevar.cov.txt |
| tabix -s 1 -b 2 -e 2 -c "#" study1.singlevar.cov.txt.gz | | tabix -s 1 -b 2 -e 2 -c "#" study1.singlevar.cov.txt.gz |
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| + | Files containing summary statistics and LD matrices generated by '''rvtests''' should be compressed and [http://samtools.sourceforge.net/tabix.shtml '''tabix'''] indexed using the following commands: |
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| + | bgzip study1.MetaScore.assoc |
| + | tabix -s 1 -b 2 -e 2 -S 1 study1.singlevar.score.txt.gz |
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| =====List of Studies===== | | =====List of Studies===== |
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| ==== QC Options ==== | | ==== QC Options ==== |
− | * '''rareMETAL''' allows filtering of variants from individual studies by their HWE pvalue and call rate, which are generated as part of the output from '''rareMetalWorker'''. | + | * '''rareMETAL''' allows filtering of variants from individual studies by their HWE pvalue and call rate, which are generated as part of the output from '''rareMetalWorker''' or [http://genome.sph.umich.edu/wiki/Rvtests '''rvtests''']. |
| * To filter by HWE p-values, --hwe option should be used. The default is 0.0, which means not filtering any of the variants. | | * To filter by HWE p-values, --hwe option should be used. The default is 0.0, which means not filtering any of the variants. |
| * To filter by call rate, --callRate option can be specified. The default is 0.0, which allows no filtering utilized. | | * To filter by call rate, --callRate option can be specified. The default is 0.0, which allows no filtering utilized. |
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| [http://genome.sph.umich.edu/wiki/Tutorial:_RareMETAL '''RAREMETAL Tutorial'''] | | [http://genome.sph.umich.edu/wiki/Tutorial:_RareMETAL '''RAREMETAL Tutorial'''] |
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| + | * For a brief tutorial of rvtests, please go to: |
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| + | [http://genome.sph.umich.edu/wiki/Rvtests '''rvtests'''] |
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| ==CONTACT== | | ==CONTACT== |