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62 bytes removed, 02:20, 14 July 2014
Single Variant Analysis
./famrvtest --ped your.ped --dat your.dat --vcf your.vcf.gz --SingleVarScore --inverseNormal --useCovariates --traitName LDL
Futhermore, if you want to run likelihood ratio test and wald test at the same time, the following command should do the work:
./famrvtest --ped your.ped --dat your.dat --SingleVarScore --SingleVarLRT --SingleVarWald --inverseNormal --useCovariates --traitName LDL
All the above commands will let you do family-based association analysis using kinship matrices generated using pedigree structure coded in pedigree file. The following command lines show examples of using genotype to estimate empirical relationship matrix to do the work.
./famrvtest --ped your.ped --dat your.dat --SingleVarScore --SingleVarLRT --SingleVarWald --inverseNormal --useCovariates --traitName LDL --kinGeno
===Gene-level Association===

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