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RAREMETAL Documentation (view source)

Revision as of 13:22, 20 May 2019

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[[Category:RAREMETAL]]
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== Useful Wiki Pages ==
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== Useful Wiki Pages ==
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* Git hub page: https://github.com/statgen/Raremetal
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There are several pages in this Wiki that may be useful to RAREMETAL users. Here are links to key pages:
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* The [[RAREMETAL_Change_Log | Change Log]]
    
* The [[RAREMETAL_DOWNLOAD_%26_BUILD | DOWNLOAD page]]
 
* The [[RAREMETAL_DOWNLOAD_%26_BUILD | DOWNLOAD page]]
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* The [[RAREMETAL|RAREMETAL Home Page]]
      
* The [[Tutorial:_RAREMETAL|RAREMETAL Quick Start Tutorial]]
 
* The [[Tutorial:_RAREMETAL|RAREMETAL Quick Start Tutorial]]
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* The [[RAREMETAL METHOD]]
    
* 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.
      
== 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.
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'''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.
    
'''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''']].
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== Key Features ==
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'''RAREMETAL''' has the following features:
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* 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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* Performs single variant metal-analysis by default.
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* Allows customized groups of variants to be tested.
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* Allows conditional analysis to be performed in both gene-level meta-analysis and single variants meta-analysis.
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* Generate QQ plots and manhattan plots by default.
    
== Approach ==
 
== Approach ==
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== Download and Installation ==
 
== Download and Installation ==
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* 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.  
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We have tested compilation using our source code on several platforms including Linux, and Mac OS X.  
    
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''']].
    
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]]
      
== Basic Usage Instructions ==
 
== Basic Usage Instructions ==
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=====Summary Statistics=====
 
=====Summary Statistics=====
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Files containing summary statistics and LD matrices generated by '''RAREMETALWORKER''' should be compressed and [http://samtools.sourceforge.net/tabix.shtml '''tabix'''] indexed using the following commands (Note in RAREMETALWORKER, if --zip is specified these .gz and .tbi files will be automatically generated):
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Files containing summary statistics and LD matrices generated by '''RAREMETALWORKER''' should be compressed and [http://samtools.sourceforge.net/tabix.shtml '''tabix'''] indexed using the following commands (Note in RAREMETALWORKER, if --zip is specified, these .gz and .tbi files will be automatically generated):
    
  bgzip study1.singlevar.score.txt
 
  bgzip study1.singlevar.score.txt
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* The above example study name file guides '''RAREMETAL''' to look for summary statistics from TwinsUK study only, because "HUNT" study is commented out. The following two files are needed for '''RAREMETAL''' to perform further analysis together with their tabix index file are needed.
 
* The above example study name file guides '''RAREMETAL''' to look for summary statistics from TwinsUK study only, because "HUNT" study is commented out. The following two files are needed for '''RAREMETAL''' to perform further analysis together with their tabix index file are needed.
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* Please sepcify --dosage option if input files were generated from dosage instead of genotype.
    
=====Group Rare Variants=====
 
=====Group Rare Variants=====
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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.
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* 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====
 
==== Conditional Analysis====
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* The annotated VCF file should be specified using --annotatedVcf option.  
 
* 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:
 
* --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:
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* (! only available after v4.13.8) when --annotation is not specified, raremetal groups all non-intergenic variants.
    
   --annotatedVcf your.annotated.vcf --annotation nonsyn/splicing
 
   --annotatedVcf your.annotated.vcf --annotation nonsyn/splicing
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==CONTACT==
 
==CONTACT==
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Please email Shuang Feng (sfengsph at umich dot edu) for questions.
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Please email Andy Boughton (abought at umich dot edu) for questions.
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== Change Log ==
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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
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* 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)
 
Abought
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