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| + | [[Category:RAREMETAL]] |
| + | == Useful Wiki Pages == |
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− | == Useful Wiki Pages ==
| + | * Git hub page: https://github.com/statgen/Raremetal |
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| * The [[RAREMETAL_Change_Log | Change Log]] | | * The [[RAREMETAL_Change_Log | Change Log]] |
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| * The [[Tutorial:_RAREMETAL|RAREMETAL Quick Start Tutorial]] | | * The [[Tutorial:_RAREMETAL|RAREMETAL Quick Start Tutorial]] |
| + | * The [[RAREMETAL METHOD]] |
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| * The [[RAREMETAL FAQ]] | | * The [[RAREMETAL FAQ]] |
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| The [http://genome.sph.umich.edu/wiki/Rvtests '''rvtests'''] tool for rare-variant association analysis can also generate output compatible with RAREMETAL. | | The [http://genome.sph.umich.edu/wiki/Rvtests '''rvtests'''] tool for rare-variant association analysis can also generate output compatible with RAREMETAL. |
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− | == Key Features ==
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− | '''RAREMETAL''' has the following features:
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− | * '''RAREMETAL''' performs gene-based or region-based meta analysis using Burden tests with the following methods: CMC_counts, Madsen-Browning, SKAT, and Variable Threshold.
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− | * '''RAREMETAL''' performs single variant metal-analysis by default.
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− | * '''RAREMETAL''' allows customized groups of variants to be tested.
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− | * '''RAREMETAL''' allows conditional analysis to be performed in both gene-level meta-analysis and single variants meta-analysis.
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− | * '''RAREMETAL''' generate QQ plots and manhattan plots by default.
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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''']] or [http://genome.sph.umich.edu/wiki/Rvtests '''rvtests'''], handles related and unrelated individuals, and supports both single variant and burden meta-analysis. '''RAREMETAL''' generates 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. It 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. It generates 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 written by Dajiang Liu using the same methodology is [[RareMetals|'''available''']]. | | '''RAREMETAL''' is developed by Shuang Feng, Dajiang Liu and Gonçalo Abecasis. A R-package written by Dajiang Liu using the same methodology is [[RareMetals|'''available''']]. |
| + | |
| + | == Key Features == |
| + | '''RAREMETAL''' has the following features: |
| + | * Performs gene-based or region-based meta analysis using Burden tests with the following methods: CMC_counts, Madsen-Browning, SKAT, and Variable Threshold. |
| + | * Performs single variant metal-analysis by default. |
| + | * Allows customized groups of variants to be tested. |
| + | * Allows conditional analysis to be performed in both gene-level meta-analysis and single variants meta-analysis. |
| + | * Generate QQ plots and manhattan plots by default. |
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| == Approach == | | == Approach == |
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| == Download and Installation == | | == Download and Installation == |
− | * University of Michigan CSG users can go to the following:
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− | /net/wonderland/home/saichen/Raremetal/
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− | === Where to Download ===
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− | We have tested compilation using our source code on several platforms including Linux, MAC OS X, and Windows. | + | We have tested compilation using our source code on several platforms including Linux, and Mac OS X. |
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| For source code and executables together with instructions of building from source, please go to [[RAREMETAL_DOWNLOAD_%26_BUILD |'''DOWNLOAD source and executables''']]. | | For source code and executables together with instructions of building from source, please go to [[RAREMETAL_DOWNLOAD_%26_BUILD |'''DOWNLOAD source and executables''']]. |
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| ==CONTACT== | | ==CONTACT== |
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− | Please email Sai Chen (saichen at umich dot edu) for questions. | + | Please email Andy Boughton (abought at umich dot edu) for questions. |
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| Also check [[Raremetal Incoming updates | '''Known issues and incoming update in next version''']] to see if your problem has been reported before | | Also check [[Raremetal Incoming updates | '''Known issues and incoming update in next version''']] to see if your problem has been reported before |