Use the option -gfile to specify the file that contains the external genetic variables. The burden score may be determined externally (default) or internally. The genetic variable pertains to the genotype in the single-variant analysis and to the burden score in the rare-variant analysis. A table in the OPTIONS section below summarizes the available analysis options for different sampling schemes. For random sampling, all traits are treated as secondary (because the sampling does not depend on any particular trait.) The sampling scheme is specified through the option -sampling. SCORE-SeqTDS performs the LS analysis on secondary quantitative traits for random sampling, case-control and case-only sampling. The LS method is the ideal choice for random sampling and is approximately correct for analyzing secondary quantitative traits in case-control or case-only studies with rare diseases. The MLE method properly accounts for trait-dependent sampling whereas the LS method does not. Both the maximum likelihood estimation (MLE) and standard least-squares (LS) methods are available. Each quantitative trait is related to a genetic variable and possibly covariates through a linear regression model. The primary trait is the trait that is used to select subjects for sequencing, and all other traits are treated as secondary. (2013) for analyzing primary and secondary quantitative traits under trait-dependent sampling. SCORE-SeqTDS is a command-line program written in the C language to implement the methods described in Lin et al. SCORE-SeqTDS: Score Tests for Sequencing Studies with Trait-Dependent Sampling
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