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− | | + | [[Category:RAREMETAL]] |
| == Useful Wiki Pages == | | == Useful Wiki Pages == |
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− | There are several pages in this Wiki that may be useful to RAREMETAL users. Here are links to key 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 [[RAREMETAL_DOWNLOAD_%26_BUILD | DOWNLOAD page]] | | * The [[RAREMETAL_DOWNLOAD_%26_BUILD | DOWNLOAD page]] |
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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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| For questions about compilation, please go to [[RAREMETAL_FAQ | '''FAQ''']]. | | For questions about compilation, please go to [[RAREMETAL_FAQ | '''FAQ''']]. |
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− | === How to Execute ===
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− | * Go to raremetal_0.4.9/raremetal/bin and use the following:
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− | ./raremetal
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− | * For example usage, please refer to [[http://genome.sph.umich.edu/wiki/Rare-Metal#Example_Usage example command lines]]
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| == Basic Usage Instructions == | | == Basic Usage Instructions == |
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| * 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. | | * 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. | | * --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 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. | + | * 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. |
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| ==== Conditional Analysis==== | | ==== Conditional Analysis==== |
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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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− | == Change Log ==
| + | Also check [[Raremetal Incoming updates | '''Known issues and incoming update in next version''']] to see if your problem has been reported before |
− | * Version 0.0.1 released to U of M CSG group. (2/13/2013)
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− | * Version 0.0.1 released. (2/24/2013)
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− | * Version 0.1.2 released after fixing a few bugs, adding conditional analysis and automatic graphing to the tool. (8/5/2013)
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− | * Version 0.2.9 released after fixing a bug in SKAT and writing PDF when all variants are monomorphic. (10/7/2013)
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− | * Version 0.3.1 released to fix a bug when one of the alleles coded as missing.
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− | * Version 0.4.0 released with a few bugs fixed to properly handling missing genotypes. Major change in command options. Now allow user to specify list of summary statistics files and covariance files separately using --summaryFiles and --covFiles options.
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− | * 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.
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− | * Version 0.4.4 released with a bug fixed when alleles are flipped in group file. (3/14/2014)
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− | * Merged raremetal and raremetalworker in one package following version number of raremetalworker. Completed testing compiling on various platforms. (4/22/14)
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