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RAREMETAL Documentation

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[[Category:RAREMETAL]]
== Useful Wiki Pages ==
== Useful Wiki Pages ==* Git hub page: https://github.com/statgen/Raremetal
* The [[RAREMETAL_Change_Log | Change Log]]
* The [[Tutorial:_RAREMETAL|RAREMETAL Quick Start Tutorial]]
* The [[RAREMETAL METHOD]]
* The [[RAREMETAL FAQ]]
The [http://genome.sph.umich.edu/wiki/Rvtests '''rvtests'''] tool for rare-variant association analysis can also generate output compatible with RAREMETAL.
 
== Key Features ==
'''RAREMETAL''' has the following features:
* '''RAREMETAL''' performs gene-based or region-based meta analysis using Burden tests with the following methods: CMC_counts, Madsen-Browning, SKAT, and Variable Threshold.
* '''RAREMETAL''' performs single variant metal-analysis by default.
* '''RAREMETAL''' allows customized groups of variants to be tested.
* '''RAREMETAL''' allows conditional analysis to be performed in both gene-level meta-analysis and single variants meta-analysis.
* '''RAREMETAL''' generate QQ plots and manhattan plots by default.
== Brief Description ==
'''RAREMETAL''' is a computationally efficient tool for meta-analysis of rare variants using sequencing or genotyping array data. '''RAREMETAL''' 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. '''RAREMETAL''' It generates high quality plots by default and has options that allow users to build reports at different levels.
'''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.
== Approach ==
== Download and Installation ==
* University of Michigan CSG users can go to the following:
/net/wonderland/home/saichen/Raremetal/
=== Where to Download === We have tested compilation using our source code on several platforms including Linux, MAC and Mac OS X, and Windows.
For source code and executables together with instructions of building from source, please go to [[RAREMETAL_DOWNLOAD_%26_BUILD |'''DOWNLOAD source and executables''']].
For questions about compilation, please go to [[RAREMETAL_FAQ | '''FAQ''']].
 
=== How to Execute ===
* Go to raremetal_0.4.9/raremetal/bin and use the following:
./raremetal
* For example usage, please refer to [[http://genome.sph.umich.edu/wiki/Rare-Metal#Example_Usage example command lines]]
== Basic Usage Instructions ==
==CONTACT==
Please email Sai Chen Andy Boughton (saichen abought at umich dot edu) for questions. Also check [[Raremetal Incoming updates | '''Known issues and incoming update in next version''']] to see if your problem has been reported before
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