SCORE-SeqTDS is a command-line program which implements the score tests described in Lin et al. (2012) for analyzing primary and secondary quantitative traits in sequencing studies with trait-dependent sampling. The primary trait is the quantitative trait that is used to select subjects for sequencing, and all other traits are treated as secondary. The selection depends on the primary trait and possibly also on covariates. Both the maximum likelihood estimation (MLE) and standard least-squares (LS) methods are available. The MLE method properly accounts for trait-dependent sampling whereas the LS method does not. 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.
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Dan-Yu Lin, Donglin Zeng, and Zheng-Zheng Tang (2013).
Quantitative Trait Analysis in Sequencing Studies With Trait-Dependent Sampling.
Proc Natl Acad Sci U S A. 2013 Jul 23;110(30):12247-52. doi: 10.1073/pnas.1221713110.