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Revision as of 22:12, 5 February 2013
, 22:12, 5 February 2013no edit summary
After you have performed the imputation, you can directly use MACH output to assess association for quantitative and qualitative traits in unrelated.
After you have performed the imputation, you can directly use MACH output to assess association for quantitative and qualitative traits in unrelated.
You will need a *.ped and *.dat files in Merlin format[http://www.sph.umich.edu/csg/abecasis/merlin/tour/input_files.html] that contain the disesase status or quantitative trait of interest (indicated with A and T respectively in the dat file)
You will need the *.ped and *.dat files in Merlin format[http://www.sph.umich.edu/csg/abecasis/merlin/tour/input_files.html] to specify the disesase status or quantitative trait of interest (indicated with A and T respectively in the dat file).
Then, you can run the association using the following command line:
*Please note that mach2dat analyze only unrelated samples. If you input family relationship, those will be ignored.
*Please note that mach2dat analyze only unrelated samples. If you input a pedigree with family relationship, those will be ignored.
If you have family data, you can use merlin-offline [http://www.sph.umich.edu/csg/abecasis/merlin/index.html]
If you have family data, you can use merlin-offline [http://www.sph.umich.edu/csg/abecasis/merlin/index.html]
== where to download ==
Please go to Li software page [http://www.unc.edu/~yunmli/software.html] for the latest version.
