FamRvTest command
From Genome Analysis Wiki
Useful Pages
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