GDT on Helix
GDT is a generalized family-based association test for dichotomous traits developed by Chen, WM etc. GDT examines the allele frequency differences in all phenotypically discordant relative pairs in general pedigrees (including large extended pedigrees with missing founders), and generalizes several "within-family association" tests such as TDT and PDT.
Sample Session on Helix
GDT sample files can be copied from:
/usr/local/gdt/ex.tar
Put these sample files under user's own area:
% mkdir /data/user/gdt/run1; cd /data/user/gdt/run1 ; cp /usr/local/gdt/ex.tar .; tar xvf ex.tar
To run gdt:
% gdt -d ex.dat -p ex.ped -m ex.map --stop 3 --cov sex --gdt
