Question: GTOOL and Plink: Single Dosage Probabilities
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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.

ADD COMMENTlinkeditmoderate 7 months ago JourneyToAbyss • 70
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1

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.

ADD REPLYlinkeditmoderate 7 months ago
zx8754
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