QTDT is a tool for the analysis of linkage disequilibrium (LD) of Quantitative and Discrete Traits. The QTDT has algorithms for exact p-values by permutation although when testing multiple linked polymorphisms, tests described by Allison (TDTQ5, 1997), Rabinowitz (1997), Monks et al. (1998), Fulker et al. (1999), and association models: Abecasis (2000), the models of Allison (1997, TDTQ5), Rabinowitz (1997), Monks (1998) and Fulker (2000).
Abecasis GR, Cardon LR, Cookson WO "A general test of association for quantitative traits in nuclear families." Am J Hum Genet. 2000 Jan;66(1):279-92. https://doi.org/10.1086/302698
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