FamRvTest command

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Revision as of 01:38, 14 July 2014 by Shuang Feng (talk | contribs) (Overview of Options)
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Useful Pages

famRvTest Home Page

famRvTest Tutorial

Overview of Options

Options:

       Kinship Options : --kinGeno, --kinPedigree, --kinFile [], --kinSave,
                         --kinMaf [0.05], --kinMiss [0.05]
  Input/Output Options : --ped [], --dat [], --vcf [], --noeof,
                         --groupFile [], --longOutput [ON], --prefix []
            VC Options : --inverseNormal, --useCovariates, --traitName []
  Single Variant Tests : --SingleVarScore
          Burden Tests : --burden, --MB, --VT, --SKAT_BETA, --SKAT_UW,
                         --SKAT_MB
         Other Options : --freqFile [], --annotation [], --maf [0.05],
                         --miss [0.05], --simulate, --dosage, --founderFreq
             PhoneHome : --noPhoneHome, --phoneHomeThinning [100]

Kinship Options

--kinGeno: kinship matrix is estimated from genotype --kinPedigree: kinship matrix is estimated from pedigree structure --kinFile: kinship matrix is read from a file --kinMaf: the maf cutoff for markers used to estimate kinship --kinMiss: the genotype call rate cutoff for markers included to estimate kinship

Input/Output Options

--ped