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, 11:59, 13 March 2014
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| * To execute the program, go to /RareMetalWorker_0.4.3/RareMetalWorker/bin, then the program can be executed by ./raremetalworker. | | * To execute the program, go to /RareMetalWorker_0.4.3/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 as following: |
− | ./raremetalworker --ped your.pheno.ped --dat your.pheno.dat --vcf your.geno.vcf.gz --useCovariates --inverseNormal --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 is as following: | | * An example command line for a related sample when you have genotype info saved in PED/DAT file is as following: |
− | ./raremetalworker --ped your.ped --dat your.dat --useCovariates --inverseNormal --prefix your.study | + | ./raremetalworker --ped your.ped --dat your.dat --prefix your.study |
| * 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: |
− | ./raremetalworker --ped your.ped --dat your.dat --useCovariates --inverseNormal --prefix your.study | + | ./raremetalworker --ped your.ped --dat your.dat --prefix your.study |
| * 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 --useCovariates --inverseNormal --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 following: |
| ./raremetalworker --ped your.pheno.ped --dat your.pheno.dat --vcf your.geno.vcf.gz --makeResiduals --useCovariates --inverseNormal --prefix your.study | | ./raremetalworker --ped your.pheno.ped --dat your.pheno.dat --vcf your.geno.vcf.gz --makeResiduals --useCovariates --inverseNormal --prefix your.study |