From Genome Analysis Wiki
→Single Variant Analysis
The following command lines let you run single variant association analysis of trait "LDL" using score test, after inverse normalization of the quantitative trait and adjusting covariates. --traitName specifies the single trait or traits you want to analyze in this batch. If this option is not used, then all traits coded in data file will be analyzed accordingly. --SingleVarLRT provides essentially the same test as in merlin --fastAssoc option.
./famrvtest --ped your.ped --dat your.dat --vcf your.vcf.gz --SingleVarScore --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.