9
edits
Changes
From Genome Analysis Wiki
Jump to navigationJump to searchMach2dat: Association with MACH output (view source)
Revision as of 22:20, 29 August 2010
, 22:20, 29 August 2010→Association with MACH output
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 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)
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:
You can also add covariates to the phenotype *ped and *dat files if you want to adjust your test for other variables.
You can also add covariates to the phenotype *ped and *dat files if you want to adjust your test for other variables.
