Tutorial: RAREMETAL

Introduction

In this tutorial, we will show how to run RareMetalWorker and RareMETAL to perform meta analysis using example data sets.

RareMetalWorker is the pre-processing tool to analyze data from individual studies and generate summary statistics for further meta analysis using RareMETAL.

RareMETAL is the tool to do gene-level meta analysis.

STEP 1: Install Software and Download Example Data Sets

• If RareMETAL and RareMetalWorker have not been installed on your local computer yet, please follow the following directions for installation. Install RareMetalWorker, Install RareMETAL
• Download the example data set for RareMetalWorker to your local drive: RareMetalWorker example data sets
• Go to your local path where the tar ball was saved then extract

 tar xvzf raremetalworker.tutorial.tgz #extract
 cd rmw_tutorial 

• Download the example data set for RareMetal to your local drive: RareMetalWorker example data sets
• Go to your local path where the tar ball was saved then extract

 tar xvzf raremetal.tutorial.tgz #extract
 cd raremetal_tutorial

STEP 2: Run RareMetalWorker on Individual Studies

• The first example has 743 individuals coded as unrelated according to PED file (each person belongs to an individual family).
• there are ~1000 markers included in the VCF file.
• To analyze this sample accounting for hidden relatedness, an empirical kinship should be calculated.
• By using the following command, covariates are adjusted and residuals are inverse normalized on the fly.

 $yourPath/bin/raremetalworker --ped $yourLocalPath/rmw_tutorial/inputfiles/example1.ped --dat $yourLocalPath/rmw_tutorial/inputfiles/example1.dat --vcf  
       $yourLocalPath/rmw_tutorial/inputfiles/example1.vcf.gz --kinGeno --kinSave --traitName LDL --inverseNormal --makeResiduals --useCovariates 
       --prefix $yourLocalPath/rmw_tutorial/outputfiles/example1

• The second sample can also be analyzed in the same fashion using the following command:

 $yourPath/bin/raremetalworker --ped $yourLocalPath/rmw_tutorial/inputfiles/example2.ped --dat $yourLocalPath/rmw_tutorial/inputfiles/example2.dat --vcf  
       $yourLocalPath/rmw_tutorial/inputfiles/example2.vcf.gz --kinGeno --kinSave --traitName LDL --inverseNormal --makeResiduals --useCovariates 
       --prefix $yourLocalPath/rmw_tutorial/outputfiles/example2

• After the two runs are finished, you will see the following output files under your current path:

 example1.singlevar.score.txt
 example1.singlevar.cov.txt
 example2.singlevar.score.txt
 example2.singlevar.cov.txt

• The output file ending with singlevar.score.txt includes summary statistics of single marker score tests.
• The output file ending with singlevar.cov.txt includes summary variance-covariance matrices of score statistics.