Changes

* The [[RAREMETALWORKER|RAREMETALWORKER documentation]]

* The [[RAREMETALWORKER|RAREMETALWORKER documentation]]

== Key Features ==

== Key Features ==

== Brief Description ==

== Brief Description ==

'''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''']], handles related and unrelated individuals, and supports both single variant and burden meta-analysis. '''RAREMETAL''' generated 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. '''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''' generated 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 using the same methodology is [[RareMetals|available]]]. Manuscript for this tool is in preparation. Please contact sfengsph at umich dot edu for questions.

'''RAREMETAL''' is developed by Shuang Feng, Dajiang Liu and Gonçalo Abecasis. A R-package using the same methodology is [[RareMetals|available]]]. Manuscript for this tool is in preparation. Please contact sfengsph at umich dot edu for questions.

==== Prepare Input Files====

==== Prepare Input Files====

'''rareMETAL''' requires the following basic input files: summary statistics and covariance matrices of score statistics generated by '''rareMetalWorker''', a file with list of studies to be included and a group file if gene-level meta-analysis is expected.  

'''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=====

=====Summary Statistics=====

  bgzip study1.singlevar.cov.txt

  bgzip study1.singlevar.cov.txt

  tabix -s 1 -b 2 -e 2 -c "#" study1.singlevar.cov.txt.gz

  tabix -s 1 -b 2 -e 2 -c "#" study1.singlevar.cov.txt.gz

=====List of Studies=====

=====List of Studies=====

==== QC Options ====

==== QC Options ====

* '''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'''.

* '''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 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.

* To filter by call rate, --callRate option can be specified. The default is 0.0, which allows no filtering utilized.

   [http://genome.sph.umich.edu/wiki/Tutorial:_RareMETAL '''RAREMETAL Tutorial''']

   [http://genome.sph.umich.edu/wiki/Tutorial:_RareMETAL '''RAREMETAL Tutorial''']

==CONTACT==

==CONTACT==