[SOLVED] ProbABEL: Which allele is the effective allele?

[wuttke]

Hi!

The ProbABEL manual states on page 15 that the A1 allele is the predictor allele.
Now it seems to me the predictor allele frequency given in column 9 of the output is my minor allele frequency, and for the SNP in question A2 is the minor allele.
May it be that the manual is wrong and A2 is the predictor allele?
I assume this does not change with the allele frequency, but is just a convention on which allele to model?

Thanks, best regards, Matthias

[wuttke]

Hi,

I think I solved it by myself.
The perl script I used to convert from Impute2 to (ml)dose format calculates the dosage of A2 instead of A1.
This caused the confusion.

Matthias

[lckarssen]

I think I solved it by myself.
The perl script I used to convert from Impute2 to (ml)dose format calculates the dosage of A2 instead of A1.
This caused the confusion.

Great! Glad to hear it's resolved.