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==STEP 2: Run RareMetalWorker on Individual Studies==
==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 also adjusted and residuals 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 example1
==STEP 3: Run RareMETAL to do Meta Analysis==
==STEP 3: Run RareMETAL to do Meta Analysis==
