GTOOL and Plink: Single Dosage Probabilities

Question

[JourneyToAbyss]

I have SNP data where each SNP is expressed as a single dosage (0...2). According to the methodology, which I am trying to replicate, gtool was used to make hard-calls and convert it to plink's .PED file format.

The schema of the SNP data is as followed....

SNP Subject 1   Subject 2   Subject 3   …
rs0001  0.001      2          1.490 
rs0002  1.002      0.3900        0  
…

As far as I can tell, gtool utilizes 3-probabilities per SNPs. Additionally, I can't think of anyway to convert single probabilities to 3-probabilities, as specified in the .GEN format.

Thus, I am wondering where I am going wrong. Perhaps there were different versions of gtool (this analysis was done 5+ years ago) or other tools/steps that I should be considering.

Answer 1

[zx8754]

As far as I know you can't go back from dosage to 3 probabilities. In other words, can you solve below?

x*0 + y*1 + z*2 = 1.49
x + y + z = 1

Plink can take --dosage as input.