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RAREMETAL Documentation

705 bytes added, 13:50, 9 October 2013
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* The [[RAREMETALWORKER|RAREMETALWORKER documentation]]
 
* The [http://genome.sph.umich.edu/wiki/Rvtests '''rvtests''']
== Key Features ==
== 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''']] 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.
==== 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. or [http://genome.sph.umich.edu/wiki/Rvtests '''rvtests''']
=====Summary Statistics=====
bgzip study1.singlevar.cov.txt
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:
 
bgzip study1.MetaScore.assoc
tabix -s 1 -b 2 -e 2 -S 1 study1.singlevar.score.txt.gz
=====List of Studies=====
==== 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'''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.
[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==
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