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--traitName QT1 --inverseNormal --makeResiduals --kinSave --kinGeno --prefix yourprefix.example2
--traitName QT1 --inverseNormal --makeResiduals --kinSave --kinGeno --prefix yourprefix.example2
==STEP 3: Run RareMETAL to do Meta Analysis==
==STEP 3: Run RAREMETAL to do Meta-Analysis==
* In this step, we run RAREMETAL to meta-analyze two studies without using any of raw data.
* First, we perform single variant and four type of gene-level meta-analysis all at once, using the following command line:
cd raremetal
$yourRAREMTALpath/bin/raremetal --studyName studyname.list --groupFile group.file --SKAT --burden --MB --VT
--longOutput --tabulateHits --hitsCutoff 1e-05 --hwe 1.0e-05 --callRate 0.95 --prefix yourprefix.QT1
* The command above allows you to gene
* A list of studies to be included is an essential piece of information for '''RareMETAL''' to run.
* A list of studies to be included is an essential piece of information for '''RareMETAL''' to run.
* First, modify the example.studyname file to make the output files of RareMetaWorker reachable by RareMETAL.
* First, modify the example.studyname file to make the output files of RareMetaWorker reachable by RareMETAL.
