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* To execute the program, go to /RareMetalWorker_0.4.8/RareMetalWorker/bin, then the program can be executed by ./raremetalworker.
* To execute the program, go to /RareMetalWorker_0.4.8/RareMetalWorker/bin, then the program can be executed by ./raremetalworker.
* An example command line for a related sample when you have genotype info saved in VCF file is as following:
* An example command line for a related sample when you have genotype info saved in VCF file is:
./raremetalworker --ped your.pheno.ped --dat your.pheno.dat --vcf your.geno.vcf.gz --prefix your.study
./raremetalworker --ped your.pheno.ped --dat your.pheno.dat --vcf your.geno.vcf.gz --prefix your.study
* An example command line for a related sample when you have genotype info saved in PED/DAT file and want to use pedigree information is as following:
* An example command line for a related sample when you have genotype info saved in PED/DAT file and want to use pedigree information is:
./raremetalworker --ped your.ped --dat your.dat --prefix your.study --kinPedigree
./raremetalworker --ped your.ped --dat your.dat --prefix your.study --kinPedigree
* An example command line for an unrelated sample when you have genotype info saved in PED/DAT file is as following:
* An example command line for an unrelated sample when you have genotype info saved in PED/DAT file is as following:
* An example command line for an unrelated sample when you have genotype info saved in VCF file is as following:
* An example command line for an unrelated sample when you have genotype info saved in VCF file is as following:
./raremetalworker --ped your.pheno.ped --dat your.pheno.dat --vcf your.geno.vcf.gz --prefix your.study
./raremetalworker --ped your.pheno.ped --dat your.pheno.dat --vcf your.geno.vcf.gz --prefix your.study
* An example command line to use when you have genotype info saved in VCF file and you want to adjust covariates first and then inverse normalize residuals is as following:
* An example command line to use when you have genotype info saved in VCF file and you want to adjust covariates first and then inverse normalize residuals is as:
./raremetalworker --ped your.pheno.ped --dat your.pheno.dat --vcf your.geno.vcf.gz --makeResiduals --inverseNormal --prefix your.study
./raremetalworker --ped your.pheno.ped --dat your.pheno.dat --vcf your.geno.vcf.gz --makeResiduals --inverseNormal --prefix your.study
* For more examples, please go to [[http://genome.sph.umich.edu/wiki/Rare-Metal-Worker#Examples Examples]].
* For more examples, please go to [[http://genome.sph.umich.edu/wiki/Rare-Metal-Worker#Examples Examples]].
