<p>Does anyone know of any software package that can convert .impute2 data to .mldose (i.e. imputed data from IMPUTE2 to imputed data from MACH)? I have tried impute2mach in GenABEL, but it has repeatedly failed with a known error...</p>

<p>Direct conversion preferred, but I&#39;m happy with indirect as long as it works!</p>

IMPUTE output is posterior probabilities, 3 columns for 1 SNP, e.g.: `0.1 0.1 0.8` corresponding to `AA AB BB`. Meaning it is more likely to be `BB`.

MACH outputs dosage, 1 column for 1 SNP, e.g.: `1.7`, corresponding `0=AA, 1=AB, 2=BB`, so `1.7` is more likely to be `BB`.

Depending on the size of the data, you can write a quick script in R that would convert posterior probabilities to dosage:

    0.1*0 + 0.1*1 + 0.8*2 = 1.7


