Mach2dat: Association with MACH output
From Genome Analysis Wiki
The printable version is no longer supported and may have rendering errors. Please update your browser bookmarks and please use the default browser print function instead.
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.
You will need the *.ped and *.dat files in Merlin format[1] 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:
mach2dat -p myfile.ped -d myfile.dat --infofile myfile.mlinfo --dosefile myfile.mldose
where myfile.mlinfo and myfile.mldose are the MACH output files.
You can also add covariates to the phenotype *ped and *dat files if you want to adjust your test for other variables.
- 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 [2]
