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Jump to navigationJump to search→STEP 2: Analyze individual samples using RAREMETALWORKER
raremetalworker --ped example1.ped --dat example1.dat --vcf example1.vcf.gz --traitName QT1
raremetalworker --ped example1.ped --dat example1.dat --vcf example1.vcf.gz --traitName QT1
--inverseNormal --makeResiduals --kinSave --kinGeno --prefix STUDY1 --labelHits
--inverseNormal --makeResiduals --kinSave --kinGeno --prefix STUDY1
This command transforms phenotypes to normality (--inverseNormal), calculates trait residuals after adjusting for covariates (--makeResiduals), estimates relatedness between individuals and saves this for later use (--kinSave and --kinGeno), and even generates some annotated PDF files summarizing results (--labelHits).
This command transforms phenotypes to normality (--inverseNormal), calculates trait residuals after adjusting for covariates (--makeResiduals), estimates relatedness between individuals and saves this for later use (--kinSave and --kinGeno), and even generates some annotated PDF files summarizing results (--labelHits).
raremetalworker --ped example2.ped --dat example2.dat --vcf example2.vcf.gz --traitName QT1
raremetalworker --ped example2.ped --dat example2.dat --vcf example2.vcf.gz --traitName QT1
--inverseNormal --makeResiduals --kinSave --kinGeno --prefix STUDY2 --labelHits
--inverseNormal --makeResiduals --kinSave --kinGeno --prefix STUDY2
==STEP 3: Run RAREMETAL for Meta-Analysis==
==STEP 3: Run RAREMETAL for Meta-Analysis==
