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RAREMETAL Documentation

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[[Category:RAREMETAL]]
== Useful Wiki Pages ==
There are several pages in this Wiki that may be useful to RAREMETAL users* Git hub page: https://github. Here are links to key pages:com/statgen/Raremetal
* The [[RAREMETAL_Change_Log | Change logLog]]
* The [[RAREMETAL_DOWNLOAD_%26_BUILD | DOWNLOAD page]]
* 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 ==
* Currently, CMC type burden test, Madsen-Browning burden test, Variable Threshold burden test and SKAT are provided in '''RAREMETAL''', by specifying --burden, --MB, --VT and --SKAT.
* --maf specifies the minor allele frequency cutoff when doing gene-based or group-based burden tests. Variants with maf '''above''' this threshold will be ignored. The default is maf<0.05.
* In '''a single study ''' of sample size N, if a site is monomorphic or not reported in vcf/ped, it is considered that the sample size of this study is not large enough to sample the rare allele. Thus, this study contributes 2*N reference alleles and 0 alternative allele towards meta-analysis. To let such studies contribute no alleles towards pooled allele frequency, specify --altMAF.
==== Conditional Analysis====
* The annotated VCF file should be specified using --annotatedVcf option.
* --annotation should be used with --annotatedVcf together when specific category of functional variants are of interest to be grouped. For example, if grouping nonsynonymous and splicing variants are of interests, the following should be included in command line:
* (! only available after v4.13.8) when --annotation is not specified, raremetal groups all non-intergenic variants.
--annotatedVcf your.annotated.vcf --annotation nonsyn/splicing
==CONTACT==
Please email Shuang Feng Andy Boughton (sfengsph abought at umich dot edu) for questions.
== Change Log ==* Version 0.0.1 released to U of M CSG group. (2/13/2013)* Version 0.0.1 released. (2/24/2013)* Version 0.1.2 released after fixing a few bugs, adding conditional analysis Also check [[Raremetal Incoming updates | '''Known issues and automatic graphing to the tool. (8/5/2013)* Version 0.2.9 released after fixing a bug incoming update in SKAT and writing PDF when all variants are monomorphic. (10/7/2013)* Version 0.3.1 released to fix a bug when one of the alleles coded as missing.* Version 0.4.0 released with a few bugs fixed to properly handling missing genotypes. Major change in command options. Now allow user next version''']] to specify list of summary statistics files and covariance files separately using --summaryFiles and --covFiles options.* Version 0.4.2 released with a bug fixed for SKAT when there are two variants in a group, and a bug fixed in Makefile for easy compiling.* Version 0.4.4 released with a bug fixed when alleles are flipped in group file. (3/14/2014)* Merged raremetal and raremetalworker in one package following version number of raremetalworker. Completed testing compiling on various platforms. (4/22/14)see if your problem has been reported before
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