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==STEP 3: Run RareMETAL to do Meta Analysis==
==STEP 3: Run RareMETAL to do Meta Analysis==
*
* 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.
cd $yourPath/raremetal_tutorial/inputfiles
* Open example.studyName and modify them into the following:
$yourLocalPath/rmw_tutorial/outputfiles/example1.LDL
$yourLocalPath/rmw_tutorial/outputfiles/example2.LDL
* If gene-level meta analysis is expected, then annotation information or groups of variants are necessary. RareMETAL can take group file to get this piece of information. * An example group file is in the following:
$yourLocaPath/raremetal_tutorial/inputfiles/nonsyn.stop.splice.groupfile
* RareMETAL also takes annotated VCF as input to parse variant grouping information. Please refer to software documentation for details [http://genome.sph.umich.edu/wiki/Rare-Metal#Grouping_from_an_Annotated_VCF_File '''grouping from annotated VCF''']
