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RAREMETAL Documentation (view source)

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'''rareMETAL''' is a tool for gene-based meta-analysis, based upon summary statistics generated from individual data using [http://genome.sph.umich.edu/wiki/Rare-Metal-Worker '''Rare Metal Worker''']. Another implementation of the same methods in R-package can be found [http://genome.sph.umich.edu/wiki/RareMETALS '''RareMetals'''].
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[[Category:RAREMETAL]]
 +
== Useful Wiki Pages ==
   −
If you have any questions, please contact: sfengsph at umich dot edu
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* Git hub page: https://github.com/statgen/Raremetal
    +
* The [[RAREMETAL_Change_Log | Change Log]]
    +
* The [[RAREMETAL_DOWNLOAD_%26_BUILD | DOWNLOAD page]]
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== Useful Wiki Pages ==
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* The [[Tutorial:_RAREMETAL|RAREMETAL Quick Start Tutorial]]
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* The [[RAREMETAL METHOD]]
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There are a few pages in this Wiki that may be useful to rareMETAL users. Here are links to key pages:
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* The [[RAREMETAL FAQ]]
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* The [[rareMETAL|rareMETAL Home Page]]
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* The [[RAREMETAL Command Reference]]
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* The [[Tutorial:_RareMETAL|rareMETAL Quick Start Tutorial]]
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* The [[RAREMETALWORKER|RAREMETALWORKER documentation]]
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* 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.
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* The [[rareMETAL Command Reference]]
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== Brief Description ==
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== Key Features ==
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'''rareMETAL''' has the following features:
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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.
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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''' generated QQ plots and manhattan plots by default.
     −
== Brief Description ==
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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 a tool for meta-analysis rare variants from genotype arrays and sequencing. rareMETAL can combine summary statistics of individual studies generated by [[Rare-Metal-Worker|rareMetalWorker]]. It provides a convenient approach for both single variant and gene-level meta-analysis of rare variants from various studies, when joint-analysis of raw data from these studies are restricted.
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== 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 ==
 
== Approach ==
   −
The key idea behind meta-analysis with rareMETAL is that various gene-level test statistics can be reconstructed from single variant score statistics and that, when the linkage disequilibrium relationships between variants are known, the distribution of these gene-level statistics can be derived and used to evaluate signifi-cance. Single variant statistics are calculated using the Cochran-Mantel-Haenszel method. The main formulae are tabulated in the following:
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The key idea behind meta-analysis with RAREMETAL is that various gene-level test statistics can be reconstructed from single variant score statistics and that, when the linkage disequilibrium relationships between variants are known, the distribution of these gene-level statistics can be derived and used to evaluate signifi-cance. Single variant statistics are calculated using the Cochran-Mantel-Haenszel method. Our method has been published in [http://www.nature.com/ng/journal/v46/n2/abs/ng.2852.html '''Liu et. al'''] in Nature Genetics. Please go to [http://genome.sph.umich.edu/wiki/RAREMETAL_method '''method'''] for details.
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{| border="1" cellpadding="5" cellspacing="0" align="center"
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|+'''Formulae for rareMETAL'''
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! scope="col" width="120pt" | Test
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! scope="col" width="50pt" | Statistics
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! scope="col" width="225pt" | Null Distribution
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|-
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| Single Variant      || <math>T=\sum_{i=1}^n {U_i}\bigg/\sqrt{\sum_{i=1}^n{V_i}}</math> || <math>T\sim\mathbf{N}(0,1)</math>
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|-
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| un-weighted Burden      || <math>T_b=\sum_{i=1}^n{\mathbf{U_i}}\Big/\sqrt{\sum_{i=1}^n{\mathbf{V_i}}}</math> || <math>T_b\sim\mathbf{N}(0,1)</math>
  −
|-
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| Weighted Burden || <math>T_{wb}=\mathbf{w^T}\sum_{i=1}^n{\mathbf{U_i}}\bigg/\sqrt{\mathbf{w^T}\left(\sum_{i=1}^n{\mathbf{V_i}}\right)\mathbf{w}}</math>  || <math>T_{wb}\sim\mathbf{N}(0,1)</math>
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|-style="height: 100pt;"
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| VT || <math>T_{VT}=\max(T_{b\left(f_1\right)},T_{b\left(f_2\right)},\dots,T_{b\left(f_m\right)}),\text{ where}</math><math>T_{b\left(f_i\right)}=\boldsymbol{\nu}_{f_i}^\mathbf{T}\sum_{i=1}^n{\mathbf{U_i}}\bigg/\sqrt{\boldsymbol{\nu}_{f_i}^\mathbf{T}\left(\sum_{i=1}^n{\mathbf{V_i}}\right)\boldsymbol{\nu}_{f_i}}\text{, where}</math> <math> \boldsymbol{\nu}_{f_i}\text{ is a indicator vector.} </math> ||<math> \left(T_{b\left(f_1\right)},T_{b\left(f_2\right)},\dots,T_{b\left(f_m\right)}\right)</math><math>\sim\mathbf{MVN}\left(\mathbf{0},\boldsymbol{\Phi}^\mathbf{T}\sum_{i=1}^n{\mathbf{V_i}}\boldsymbol{\Phi}\right)</math>
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|-
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| SKAT || <math>\mathbf{Q}=\left(\sum_{i=1}^n{\mathbf{U_i^T}}\right) \mathbf{W}\left(\sum_{i=1}^n{\mathbf{U_i}}\right)</math> ||<math>\mathbf{Q}\sim\sum_{i=1}^m{\lambda_i\chi_{1,i}^2},\text{ where}</math> <math>\left(\lambda_1,\lambda_2,\dots,\lambda_m\right)\text{ are eigen values of}</math><math>\left(\sum_{i=1}^n{\mathbf{V_i}}\right)^\frac{1}{2}\mathbf{W}\left(\sum_{i=1}^n{\mathbf{V_i}}\right)^\frac{1}{2}</math>
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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/fantasia/home/sfengsph/code/Rare-Metal/raremetal/bin/raremetal
     −
=== Where to Download ===
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We have tested compilation using our source code on several platforms including Linux, and Mac OS X.  
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* The software package for Linux and Mac (source code included) can be downloaded here: [[Media:raremetal.0.0.2.tgz|software package download]]
     −
=== How to Compile ===
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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''']].
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* Save it to your local path and decompress using the following command:
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  tar xvzf raremetal.0.0.1.tgz
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* Go to raremetal_0.0.1/raremetal/src and type the following command to compile:
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  make
     −
=== How to Execute ===
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For questions about compilation, please go to [[RAREMETAL_FAQ | '''FAQ''']].
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* Go to raremetal_0.0.1/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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raeMETAL is a command line tool. It is typically run from a Linux or Unix prompt by invoking the command <code>raremetal</code>. An example is included at the bottom of this page.
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'''RAREMETAL''' is a command line tool. It is typically run from a Linux or Unix prompt by invoking the command <code>raremetal</code>. In the following are descriptions of basic usage for meta analysis. A detailed [[Tutorial:_RareMETAL|'''TUTORIAL''']] with toy data are also available.
 +
 
 +
==== Prepare Input Files====
 +
'''RAREMETAL''' requires the following basic input files: summary statistics and covariance matrices of score statistics generated by '''RAREMETALWORKER''' or [http://genome.sph.umich.edu/wiki/Rvtests '''rvtests'''], a file with list of studies to be included and a group file if gene-level meta-analysis is expected.
 +
 
 +
 
 +
=====Summary Statistics=====
 +
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
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tabix -s 1 -b 2 -e 2 -c "#" study1.singlevar.score.txt.gz
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bgzip study1.singlevar.cov.txt
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tabix -s 1 -b 2 -e 2 -c "#" study1.singlevar.cov.txt.gz
 +
 
 +
Files containing summary statistics and LD matrices generated by '''rvtests''' should be compressed and [http://samtools.sourceforge.net/tabix.shtml '''tabix'''] indexed using the following commands:
   −
A detailed [[Tutorial:_RareMETAL|'''TUTORIAL''']] with toy data are also available.
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bgzip study1.MetaScore.assoc
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tabix -s 1 -b 2 -e 2 -S 1 study1.MetaScore.assoc.gz
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tabix -s 1 -b 2 -e 2 -S 1 study1.MetaCov.assoc.gz
   −
==== List of Studies ====
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=====List of Studies=====
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* --studyName option is crucial for '''Rare Metal''' to work. Ignoring this option will lead to FATAL ERROR and '''Rare Metal''' will stop.  
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* --summaryFiles option is crucial for '''RAREMETAL''' to work. Ignoring this option would lead to FATAL ERROR and '''RAREMETAL''' would stop.  
 
* The file should contain the path and prefix of the studies you want to include.  
 
* The file should contain the path and prefix of the studies you want to include.  
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* If there is one or more studies that you want to excluded from your list, but want to save some effort of generating a new file, you can put a "#" in front of the line of record. '''Rare Metal''' will automatically exclude that study from meta analysis.
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* If there is one or more studies that you want to excluded from your list, but want to save some effort of generating a new file, you can put a "#" in front of the line of record. '''RAREMETAL''' would automatically exclude that study from meta analysis. An example list of summary file is in the following:
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* An example file is in the following:
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 +
  /net/fantasia/home/sfengsph/prj/raremetal/raremetal/bin/META/TwinsUK/TwinsUK.TG.singlevar.score.txt.gz
 +
  #/net/fantasia/home/sfengsph/prj/raremetal/raremetal/bin/META/HUNT/RareMetalWorker/HUNT_MI_case.TG.singlevar.score.txt.gz
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  /net/fantasia/home/sfengsph/prj/raremetal/raremetal/bin/META/TwinsUK/TwinsUK.TG
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* When gene-level analysis is requested, --covFiles option should be used to specify the covariance files. An example file is:
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  #/net/fantasia/home/sfengsph/prj/raremetal/raremetal/bin/META/HUNT/RareMetalWorker/HUNT_MI_case.TG
     −
* The above example study name file guides '''Rare Metal''' looking for the following files as input (note that the second study has been opt out from the meta analysis, because of the "#" in front of the line)
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  /net/fantasia/home/sfengsph/prj/raremetal/raremetal/bin/META/TwinsUK/TwinsUK.TG.singlevar.cov.txt.gz
 +
  #/net/fantasia/home/sfengsph/prj/raremetal/raremetal/bin/META/HUNT/RareMetalWorker/HUNT_MI_case.TG.singlevar.cov.txt.gz
   −
  /net/fantasia/home/sfengsph/prj/raremetal/raremetal/bin/META/TwinsUK/TwinsUK.TG.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.
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  /net/fantasia/home/sfengsph/prj/raremetal/raremetal/bin/META/TwinsUK/TwinsUK.TG.singlevar.cov.txt
     −
==== Grouping of Rare Variants====
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* Please sepcify --dosage option if input files were generated from dosage instead of genotype.
   −
===== From a Group File =====
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=====Group Rare Variants=====
 +
 
 +
====== From a Group File ======
 
* Grouping methods are only necessary when doing gene-based or group-based burden tests in meta-analysis.  
 
* Grouping methods are only necessary when doing gene-based or group-based burden tests in meta-analysis.  
 
* If none of the grouping method is specified, then only single variant meta-analysis will be performed.  
 
* If none of the grouping method is specified, then only single variant meta-analysis will be performed.  
Line 104: Line 101:  
   C1orf159        1:1021285:G:T  1:1021302:T:C  1:1021315:A:C  1:1021386:G:A  1:1022534:C:T  1:1025751:C:T  1:1026913:C:T
 
   C1orf159        1:1021285:G:T  1:1021302:T:C  1:1021315:A:C  1:1021386:G:A  1:1022534:C:T  1:1025751:C:T  1:1026913:C:T
   −
===== From an Annotated VCF File =====
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====== From an Annotated VCF File ======
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* If --groupFile option is not specified, '''Rare Metal''' will look for an annotated vcf file as blue print for variants to group.
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If --groupFile option is '''NOT''' specified, '''RAREMETAL''' will look for an annotated vcf file as blue print for variants to group. Users are also allowed to generate a vcf file based on the superset of variants from pooled samples, and annotate outside RAREMETAL. Then, annotated vcf file can be used as input for RAREMETAL for gene-level meta-analysis, or group files can be generated based on the annotated vcf file. Detailed description of these options are [[Rare-Metal#Group_Rare_Variants_from_Annotated_VCF|'''available''']]. There are also [[Rare-Metal#Example_Command_lines|'''examples''']] of this usage at the bottom of this page.
 +
 
 +
==== QC Options ====
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* '''RAREMETAL''' allows filtering of variants from individual studies by their HWE pvalue and call rate, which are generated as part of the output from '''RAREMETALWORKER''' or [http://genome.sph.umich.edu/wiki/Rvtests '''rvtests'''].
 +
* To filter by HWE p-values, --hwe option should be used. The default is 0.0, which means not filtering any of the variants.
 +
* To filter by call rate, --callRate option can be specified. The default is 0.0, which allows no filtering utilized.
 +
 
 +
==== Association Options====
 +
* 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====
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* To decide whether a signal is caused by shadowing a significant common variant nearby, '''RAREMETAL''' also enables conditional analysis with a list of variants to be conditioned upon provided in a file as input for --condition option. An example input file should be space or tab delimited as in the following. When alleles do not match the ref and alt alleles from samples, the variant will be skipped from conditional analysis.
 +
 
 +
1:861349:C:T 1:905901:G:A 20:986998:G:C 22:3670691:A:G
 +
 
 +
== Additional Analysis Options ==
 +
 
 +
=== Generate a VCF File to Annotate Outside RAREMETAL ===
 +
* --writeVCF allows user to write a VCF file including pooled single variants from all studies. Then users can use their favorite annotation tool to annotate the VCF file. After annotating the VCF file, users can use that file as input for '''RAREMETAL''' for further gene-based or region-based meta analysis.
 +
* The output vcf file will be name as: yourPrefix.pooled.variants.vcf. An example output vcf file is in the following:
 +
  #CHROM    POS    ID      REF    ALT    QUAL    FILTER  INFO
 +
  1      115658497      115658497      G      A      .      .      ALT_AF=0.380906;
 +
  2      74688884        74688884        G      A      .      .      ALT_AF=8.33611e-05;
 +
  3      121414217      121414217      C      A      .      .      ALT_AF=0.0747833;
 +
===Annotation===
 +
* RAREMETAL automatically recognizes the annotation format generated by [[TabAnno | '''ANNO''']] or [[EPACTS#Annotating_VCF_file_using_EPACTS | '''EPACTS''']].
 +
* To annotate a the VCF generated in previous step, you can use the following command:
 +
./anno --in your.in.vcf.gz --out your.out.vcf.gz
 +
 
 +
=== Group Rare Variants from Annotated VCF ===
 +
* If --groupFile option is '''NOT''' specified, '''RAREMETAL''' will look for an annotated vcf file as blue print for variants to group.
 
* 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:
 +
* (! 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
Line 122: Line 152:     
* Notice that each variant is allowed to have more than one annotations; but each annotation should start with a new key "ANNO=" followed by annotation:genename:other transcript information.
 
* Notice that each variant is allowed to have more than one annotations; but each annotation should start with a new key "ANNO=" followed by annotation:genename:other transcript information.
 +
* Generated group file will be named test.groupfile under your running directory.
   −
===== Generate a VCF File to Annotate Outside of Rare Metal =====
+
===Options for Report Generation===  
−
* --writeVCF allows user to write a VCF file including pooled single variants from all studies. Then users can use their favorite annotation tool to annotate the VCF file. After annotating the VCF file, users can use that file as input for '''Rare Metal''' for further gene-based or region-based meta analysis.
+
* --correctGC generates QQ plots and manhattan plots with pvalues corrected using genomic control.
−
* The output vcf file will be name as: yourPrefix.pooled.variants.vcf. An example output vcf file is in the following:
  −
  #CHROM    POS    ID      REF    ALT    QUAL    FILTER  INFO
  −
  1      115658497      115658497      G      A      .      .      ALT_AF=0.380906;
  −
  2      74688884        74688884        G      A      .      .      ALT_AF=8.33611e-05;
  −
  3      121414217      121414217      C      A      .      .      ALT_AF=0.0747833;
  −
 
  −
==== QC Options ====
  −
* '''Rare Metal''' allows filtering of variants from individual studies by their HWE pvalue and call rate, which are generated as part of the output from '''Rare Metal Worker'''.
  −
* To filter by HWE p-values, --hwe option should be used. The default is 0.0, which means not filtering any of the variants.
  −
* To filter by call rate, --callRate option can be specified. The default is 0.0, which allows no filtering utilized.
  −
 
  −
==== Association Methods ====
  −
* Currently, four methods are provided in '''Rare Metal''', CMC type burden test, Madsen-Browning burden test, Variable Threshold burden test, and SKAT.
  −
 
  −
== Additional Analysis Options ==
   
* --prefix allows customized prefix for output files.  
 
* --prefix allows customized prefix for output files.  
−
* --maf specifies the minor allele frequency cutoff when doing gene-based or group-based burden tests. The default is maf<0.05.
   
* --longOutput allows users to output not only burden test results but also the single variant results (allele frequencies, effect sizes, and p-values) for the variants being grouped together. Please refer to the output files section for detailed explanation and examples.
 
* --longOutput allows users to output not only burden test results but also the single variant results (allele frequencies, effect sizes, and p-values) for the variants being grouped together. Please refer to the output files section for detailed explanation and examples.
−
* --tabulateHits works with --hitsCutoff together to generate reports for genes that have p-value less than specified cutoff from burden tests or SKAT. The default cutoff of p-value for genes to be reported is 1.0e-06, which can be specified by --hitsCutoff option. For more explanations and examples, please go to [[http://genome.sph.umich.edu/wiki/Rare-Metal#Tabulated_Top_Hits Tabulated Top Hits]].
+
* --tabulateHits works with --hitsCutoff together to generate reports for genes that have p-value less than specified cutoff from burden tests or SKAT. The default cutoff of p-value for genes to be reported is 1.0e-06, which can be specified by --hitsCutoff option. For more explanations and examples, please go to [[Rare-Metal#TABULATED_HITS| Tabulated Hits]].
−
 
  −
== Input Files ==
  −
Rare Metal needs the following as input:
  −
 
  −
==== List of Studies ====
  −
* A file with the path and name of files containing summary statistics generated by raremetalworker should be specified.
  −
* If no such file is provided, '''Rare Metal''' will stop and report FATAL ERROR.
  −
* Please go to [[http://genome.sph.umich.edu/wiki/Rare-Metal#List_of_Studies_2 example input for study names]] for detailed explanation and examples.
  −
 
  −
==== Groups of Variants ====
  −
To perform gene-based or group-based burden test, groups of variants need to be provided. There are two options to provide such information:
  −
 
  −
=====From Group File =====
  −
* A group file contains the list of groups or genes with the variants to be included in your burden tests.
  −
* Please refer to the instruction of --groupFile option for formats and examples.
  −
 
  −
=====From Annotated VCF File =====
  −
* '''rareMETAL''' allows user to use annotated VCF file as input for grouping of variants, which is optional to input a group file as described above.
  −
* '''rareMETAL''' also has the option of generating a VCF file according to the pooled information from individuals studies. Then user can use their favorite annotation tools to annotate the VCF file into the INFO field. Currently, '''rareMETAL''' only support limited formats of annotated VCF file.
  −
* A more flexible way, which is also a recommended way, is to generate a group file from the customized annotated VCF file and use that as input to '''rareMETAL'''.
  −
* For formats of annotated VCF that '''rareMETAL''' currently support, please refer to the following [http://genome.sph.umich.edu/wiki/Rare-Metal#Grouping_from_an_Annotated_VCF_File  annotated VCF]:
  −
 
  −
'''NOTE:''' if no grouping method is provided, then only single variant meta analysis will be performed.
  −
 
  −
 
      +
===Miscellaneous Options===
 +
* --tabix allows rapid analysis when number of groups/genes of interests are small. Currently, when number of groups is less than 100, --tabix option is automatically turned on.
    +
== Reports Generated by RAREMETAL ==
 +
=== Single Variant Meta Analysis Output ===
   −
== Results Reported by rareMETAL ==
+
==== TABLES ====
−
=== Single Variant Meta Analysis Output ===
     −
* Single variant meta analysis output has the following components: header and results.  
+
* Single variant meta analysis output has the following components: header, results and footnote.  
 
* Header lines start with "##" shows summary of the meta analysis including method used, number of studies, and total sample size.  
 
* Header lines start with "##" shows summary of the meta analysis including method used, number of studies, and total sample size.  
 
* Header line starts with "#" are column headers for results table.
 
* Header line starts with "#" are column headers for results table.
 +
* Footnote also starts with "#", where genomic controls from each study and the overall sample are reported.
 
* An example single variant meta analysis output is shown below:
 
* An example single variant meta analysis output is shown below:
   Line 197: Line 191:  
   EFFECT_SIZE:        Alternative Allele Effect Size
 
   EFFECT_SIZE:        Alternative Allele Effect Size
 
   DIRECTION_BY_STUDY: Effect size direction of alternative allele from each study.  
 
   DIRECTION_BY_STUDY: Effect size direction of alternative allele from each study.  
−
                       The order of study is consistent with the order of studies listed in the input file for option --studyName.  
+
                       The order of study is consistent with the order of studies listed in the input file for option --summaryFiles.  
 
                       "?" means the variant is not observed or monomorphic from the study.  
 
                       "?" means the variant is not observed or monomorphic from the study.  
 
                       "!" means the variant observed from this study has different alleles from those in the first study.
 
                       "!" means the variant observed from this study has different alleles from those in the first study.
   −
=== Burden Tests Meta Analysis Output ===
+
==== PLOTS====
−
When --longOutput is specified, output includes both burden test results of genes and single variant results of the variants included in burden tests. Otherwise, single variant results of variants included in burden tests will not be included in the output.
+
 
 +
'''RAREMETAL''' generates QQ plots and manhattan plots from single variant meta-analysis by default. Three QQ plots are generated, one with all variants included, one of variants with maf<0.05 and one of variants with maf<0.01. All plots are saved in a pdf file named yourPrefix.meta.plots.pdf. Genomic controls are also reported in the title of plots. When --correctGC option is specified, GC corrected plots are also generated.
 +
{| border="1" cellpadding="5" cellspacing="0" align="center"
 +
|-
 +
| align="center" width="100" | [[File:QQ.png]]
 +
|-
 +
| align="center" width="200" | [[File:Single_var_manhattan.png]]
 +
|}
 +
 
 +
=== Gene-level Tests Meta-Analysis Output ===
   −
==== Long Output Format ====
+
 
−
* Here is an example of output file from SKAT when --longOutput is specified.  
+
==== LONG TABLES ====
 +
When --longOutput is used, output includes both burden test results of genes and single variant results of the variants included in burden tests. Here is an example of output file from SKAT when --longOutput is specified.  
 
   ##Method=Burden
 
   ##Method=Burden
 
   ##STUDY_NUM=2
 
   ##STUDY_NUM=2
Line 213: Line 217:  
   KLHL17  2      1:897285:A:G;1:898869:C:T      0.0148408,0.00108369    -0.0502034,-0.0256403  0.528269,0.934606      0.00796222      0.00108369      0.0148408      -0.0484494      0.528878
 
   KLHL17  2      1:897285:A:G;1:898869:C:T      0.0148408,0.00108369    -0.0502034,-0.0256403  0.528269,0.934606      0.00796222      0.00108369      0.0148408      -0.0484494      0.528878
   −
====Short Output Format ====
+
==== SHORT TABLES ====
−
* Here is an example of output file from SKAT when --longOutput is not specified.
+
Otherwise, single variant results of variants included in burden tests will not be included in the output. Here is an example of output file from SKAT when --longOutput is not specified.
    
   ##Method=Burden
 
   ##Method=Burden
Line 223: Line 227:  
   KLHL17  2      1:897285:A:G;1:898869:C:T      0.00796222      0.00108369      0.0148408      -0.0484494      0.528878
 
   KLHL17  2      1:897285:A:G;1:898869:C:T      0.00796222      0.00108369      0.0148408      -0.0484494      0.528878
   −
==== Tabulated Top Hits ====
+
==== TABULATED HITS ====
 
* When --tabulateHits is specified, top hits from Burden tests will be generated. Each method will have an individual tabulated file generated. The purpose of this tabulated file is to list burden test results of top hits together with single variant results from variants being grouped in burden tests. The difference between this file and the standard long-format output file from burden test is that each row of the file represents a single variant that is included in the gene for burden test. This format allows each sorting on users end.  
 
* When --tabulateHits is specified, top hits from Burden tests will be generated. Each method will have an individual tabulated file generated. The purpose of this tabulated file is to list burden test results of top hits together with single variant results from variants being grouped in burden tests. The difference between this file and the standard long-format output file from burden test is that each row of the file represents a single variant that is included in the gene for burden test. This format allows each sorting on users end.  
   Line 251: Line 255:  
* According to the example above, PCSK9 had a p-value of 7.54587e-11 from the gene-based burden test, where three variants from this gene were included. Another hit from this meta analysis is APOE, where only one variant was included in the burden test.
 
* According to the example above, PCSK9 had a p-value of 7.54587e-11 from the gene-based burden test, where three variants from this gene were included. Another hit from this meta analysis is APOE, where only one variant was included in the burden test.
   −
==== Log File ====
+
==== PLOTS ====
 +
'''RAREMETAL''' generates QQ plots and manhattan plots from single variant and gene-level meta-analysis by default. Example QQ plots and manhattan plots are:
 +
{| border="1" cellpadding="5" cellspacing="0" align="center"
 +
|-
 +
| align="center" width="200" | [[File:manhattan.png]]
 +
|}
   −
* A log file is automatically generated by '''Rare Metal''' to save the parameters in effect. An example is in the following:
+
==== LOG ====
 +
 
 +
* A log file is automatically generated by '''RAREMETAL''' to save the parameters in effect. An example is in the following:
    
   The following parameters are in effect:
 
   The following parameters are in effect:
Line 263: Line 274:  
   Grouping Methods:
 
   Grouping Methods:
 
   ============================
 
   ============================
−
   --groupFile []
+
   --groupFile [genes.file]
−
   --annotatedVcf [../../groupvcf/bin/debug/nonsynonymous.vcf]
+
   --annotatedVcf []
 
   --annotation []
 
   --annotation []
 
   --writeVcf [OFF]
 
   --writeVcf [OFF]
Line 279: Line 290:  
   --SKAT [false]
 
   --SKAT [false]
 
   --VT [false]
 
   --VT [false]
 +
  --condition [condition.file]
 
    
 
    
 
   Other Options:
 
   Other Options:
 
   ============================
 
   ============================
 +
  --tabix [OFF]
 +
  --correctGC [ON]
 
   --prefix [test]
 
   --prefix [test]
 
   --maf [0.05]
 
   --maf [0.05]
Line 287: Line 301:  
   --tabulateHits [false]
 
   --tabulateHits [false]
 
   --hitsCutoff [1e-06]
 
   --hitsCutoff [1e-06]
 +
  --dosage [false]
 +
  --altMAF [false]
    
==Example Command lines==
 
==Example Command lines==
    
* Here is an example command line to do single variant meta analysis only:
 
* Here is an example command line to do single variant meta analysis only:
−
   ./raremetal --studyName your.studyName.file --prefix yourPrefix  
+
   ./raremetal --summaryFiles your.list.of.summary.files --prefix yourPrefix  
    
* When you want to do all burden tests using a group file to specify which variants to group:
 
* When you want to do all burden tests using a group file to specify which variants to group:
−
   ./raremetal --studyName your.studyName.file --groupFile your.groupfile --burden --MB --SKAT --VT --maf 0.01 --prefix yourPrefix
+
   ./raremetal --summaryFiles your.list.of.summary.files --covFiles your.list.of.cov.files --groupFile your.groupfile --burden --MB --SKAT --VT --maf 0.01 --prefix yourPrefix
 
   (NOTE: this will generate single variant meta analysis result and the short format output for burden test results.)
 
   (NOTE: this will generate single variant meta analysis result and the short format output for burden test results.)
    
* Here is how to do all SKAT meta analysis using a group file and request a long format output together with tabulated hits:
 
* Here is how to do all SKAT meta analysis using a group file and request a long format output together with tabulated hits:
−
   ./raremetal --studyName your.studyName.file --groupFile your.groupfile --SKAT --longOutput --tabulateHits --hitsCutoff 1.0e-07 --prefix yourPrefix
+
   ./raremetal --summaryFiles your.list.of.summary.files --covFiles your.list.of.cov.files --groupFile your.groupfile --SKAT --longOutput --tabulateHits --hitsCutoff 1.0e-07 --prefix yourPrefix
    
* Here is an example of adding QC filters to variants when doing meta analysis.
 
* Here is an example of adding QC filters to variants when doing meta analysis.
−
   ./raremetal --studyName your.studyName.file --groupFile your.groupfile --SKAT --longOutput --tabulateHits --hitsCutoff 1.0e-07 --hwe 1e-06 --callRate 0.98 --prefix yourPrefix
+
   ./raremetal --summaryFiles your.list.of.summary.files --covFiles your.list.of.cov.files --groupFile your.groupfile --SKAT --longOutput --tabulateHits --hitsCutoff 1.0e-07 --hwe 1e-06 --callRate 0.98 --prefix yourPrefix
    
* Here is how to do the same thing but reading grouping information from an annotated VCF file:
 
* Here is how to do the same thing but reading grouping information from an annotated VCF file:
−
   ./raremetal --studyName your.studyName.file --annotatedVcf your.annotated.vcf --annotation nonsyn/stop/splicing --SKAT --longOutput --tabulateHits --hitsCutoff 1.0e-07 --hwe 1e-06 --callRate 0.98 --prefix yourPrefix
+
   ./raremetal --summaryFiles your.list.of.summary.files --covFiles your.list.of.cov.files --annotatedVcf your.annotated.vcf --annotation nonsyn/stop/splicing --SKAT --longOutput --tabulateHits --hitsCutoff 1.0e-07 --hwe 1e-06 --callRate 0.98 --prefix yourPrefix
   −
* If you want to write a VCF file of pooled variants from all studies, annotate them using your favorite annotation program, and then come back to '''Rare Metal''' with the annotate VCF file to do burden tests:
+
* If you want to write a VCF file of pooled variants from all studies, annotate them using your favorite annotation program, and then come back to '''RAREMETAL''' with the annotate VCF file to do burden tests:
 
   First, use the following command to write the VCF file:
 
   First, use the following command to write the VCF file:
−
   ./raremetal --studyName your.studyName.file --writeVcf --prefix yourPrefix
+
   ./raremetal --summaryFiles your.list.of.summary.files --writeVcf --prefix yourPrefix
−
   Second, annotate the VCF file using your favorite annotation program. (Annotated VCF file has to follow the format described here: [[http://genome.sph.umich.edu/wiki/Rare-Metal#Grouping_from_an_Annotated_VCF_File annotated VCF format]])
+
   Second, annotate the VCF file using your favorite annotation program. (Annotated VCF file has to follow the format described here: [[Rare-Metal#Group_Rare_Variants_from_Annotated_VCF|annotated VCF format]])
 
   Third, use the following command to do meta analysis:
 
   Third, use the following command to do meta analysis:
−
   ./raremetal --studyName your.studyName.file --annotatedVcf your.annotated.vcf --annotation nonsyn/splicing/stop --burden --MB --SKAT --VT --maf 0.01 --prefix yourPrefix
+
   ./raremetal --summaryFiles your.list.of.summary.files --covFiles your.list.of.cov.files --annotatedVcf your.annotated.vcf --annotation nonsyn/splicing/stop --burden --MB --SKAT --VT --maf 0.01 --prefix yourPrefix
 +
 
 +
==Other Useful Info==
 +
 
 +
* Summary specs can be found [[Summary Files Specification for RAREMETAL]]
    
==TUTORIAL==
 
==TUTORIAL==
−
* For a comprehensive tutorial of RareMetalWorker and RareMETAL using example data sets, please go to the following:
+
* For a comprehensive tutorial of RAREMETALWORKER and RAREMETAL using example data sets, please go to the following:
 +
 
 +
  [http://genome.sph.umich.edu/wiki/Tutorial:_RareMETAL '''RAREMETAL Tutorial''']
 +
 
 +
* For a brief tutorial of rvtests, please go to:
 +
 
 +
  [http://genome.sph.umich.edu/wiki/Rvtests '''rvtests''']
 +
 
 +
==CONTACT==
   −
  [http://genome.sph.umich.edu/wiki/Tutorial:_RareMETAL '''RareMETAL Tutorial''']
+
Please email Andy Boughton (abought at umich dot edu) for questions.
   −
== 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)
  −
* Version 0.0.1 released to public. (2/24/2013)
  −
* Version 0.1.0 released to public after fixing a few bugs, adding conditional analysis and automatic graphing to the tool. (8/5/2013)
 
Abought
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