Commit 5a7f17eb authored by zhanxw's avatar zhanxw Committed by zhanxw
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......@@ -291,11 +291,14 @@ Score test | score | B,Q | Y | R, U
Dominant model | dominant | B,Q | Y | R, U | score tests and covariance matrix under dominant disease model
Recessive model | recessive | B,Q | Y | R, U | score tests and covariance matrix under recessive disease model
Covariance | cov | B,Q | Y | R, U | covariance matrix
BOLT-LMM score test | score[bolt] | Q | Y | R, U | BOLT-LMM based score tests
(#) Model columns list the recognized names in rvtests. For example, use `--meta score,cov` will generate score statistics and covariance matrix for meta-analysis.
(##) In trait column, B or Q stand for binary or quantitative trait, respectively.
(###) This method also requires pruned gneotype data in the PLINK format specified by `--boltPlink`. A minimal example to run BOLT-LMM based score tests is: `rvtest --inVcf $inputVCFfile --boltPlink $binaryPlinkPrefix --pheno $phenotype --meta score[bolt]`.
The above models are suitable to generate summary statistics which can be later meta-analyzed (see [Dajiang Liu (2014) Nature Genetics](http://www.nature.com/ng/journal/v46/n2/abs/ng.2852.html)).
Rvtests implemented the above methods and the results can be further analyzed by RareMetals ([link](http://genome.sph.umich.edu/wiki/RareMETALS)) for quantitative trait and RareMetals2 ([link](http://genome.sph.umich.edu/wiki/RareMETALS2)).
It also worth to mention that our group offers another toolset for meta analysis ([link](http://genome.sph.umich.edu/wiki/Rare-Metal)).
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