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, 14:13, 11 April 2014
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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, issue ./raremetalworker. |
| − | * Some example command lines when you have genotype info saved in PED/DAT file are in the following. For more examples, please refer to [[RAREMETALWORKER#Example_Command_Lines | '''RAREMETALWORKER EXAMPLES''']]. | + | * For example command lines, please refer to [[RAREMETALWORKER#Example_Command_Lines | '''RAREMETALWORKER EXAMPLES''']]. |
| − | If you want to analyze the sample as unrelated individuals, then use
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| − | ./raremetalworker --ped your.ped --dat your.dat --prefix your.study (this will give your output a recognizable prefix)
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| − | If you want to analyze the sample as related using pedigree information, then use
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| − | ./raremetalworker --ped your.ped --dat your.dat --kinPedigree --prefix your.study
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| − | If you want to analyze the sample as related using genomic relationship matrix, then use
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| − | ./raremetalworker --ped your.ped --dat your.dat --kinGeno --kinSave --prefix your.study
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| − | * Some example command lines when you have genotype info saved in VCF file (you still have to save the phenotype and covariate information in PED/DAT file)
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| − | If you want to analyze the sample as unrelated individuals, then use
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| − | ./raremetalworker --ped your.ped --dat your.dat --vcf your.vcf.gz --prefix your.study
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| − | If you want to analyze the sample as related using pedigree information, then use
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| − | ./raremetalworker --ped your.ped --dat your.dat --vcf your.vcf.gz --kinPedigree --prefix your.study
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| − | If you want to analyze the sample as related using genomic relationship matrix, then use
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| − | ./raremetalworker --ped your.ped --dat your.dat --vcf your.vcf.gz --kinGeno --kinSave --prefix your.study
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| | ==Method== | | ==Method== |
