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==STEP 2: Run RareMetalWorker on Individual Studies==
==STEP 2: Run RareMetalWorker on Individual Studies==
===Example 1===
* The first example has 743 individuals coded as unrelated according to PED file (each person belongs to an individual family).
* 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.
* there are ~1000 markers included in the VCF file.
* To analyze this sample accounting for hidden relatedness, an empirical kinship should be calculated.
* 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.
* Go to $yourPath/bin/ and execute the following command:
$yourPath/bin/raremetalworker --ped rmw_tutorial/inputfiles/example1.ped
$yourPath/bin/raremetalworker --ped rmw_tutorial/inputfiles/example1.ped
--prefix rmw_tutorial/output/example1
--prefix rmw_tutorial/output/example1
--traitName QT1 --inverseNormal --makeResiduals --kinSave --kinGeno
--traitName QT1 --inverseNormal --makeResiduals --kinSave --kinGeno
Thefollowing command allows covariates to be adjusted and residuals inverse normalized.
===Example 2===
* The second sample can also be analyzed in the same fashion using the following command:
* The second sample can also be analyzed in the same fashion using the following command:
