Mach2dat: Association with MACH output

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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]