From Genome Analysis Wiki
Jump to navigationJump to search
881 bytes added
, 11:58, 14 April 2014
Line 277: |
Line 277: |
| | | |
| prompt> $PATH/bin/raremetalworker --ped yourInput.ped --dat yourInput.dat --vcf yourInput.vcf.gz --traitName BMI --prefix yourFavoritePrefix | | prompt> $PATH/bin/raremetalworker --ped yourInput.ped --dat yourInput.dat --vcf yourInput.vcf.gz --traitName BMI --prefix yourFavoritePrefix |
| + | |
| + | * If you want to inverse normalize (quantile normalize) your trait before doing associations, this can be done by adding --inverseNormal to your command line: |
| + | |
| + | prompt> $PATH/bin/raremetalworker --ped yourInput.ped --dat yourInput.dat --vcf yourInput.vcf.gz --traitName BMI --prefix yourFavoritePrefix --inverseNormal |
| + | |
| + | * The following command will adjust covariates first and then use residuals to proceed association: |
| + | |
| + | prompt> $PATH/bin/raremetalworker --ped yourInput.ped --dat yourInput.dat --vcf yourInput.vcf.gz --traitName BMI --prefix yourFavoritePrefix --makeResiduals |
| + | |
| + | * The following command will adjust covariates first and then use the inverse normalized residuals to proceed association: |
| + | |
| + | prompt> $PATH/bin/raremetalworker --ped yourInput.ped --dat yourInput.dat --vcf yourInput.vcf.gz --traitName BMI --prefix yourFavoritePrefix --makeResiduals --inverseNormal |
| | | |
| === Related individuals === | | === Related individuals === |