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
[SOLVED] ProbABEL: Which allele is the effective allele?
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The first few posts of newly registered users will be moderated in order to filter out any spammers.
When get a solution to the problem you posted, please change the topic name (e.g. from "how to ..." to "[SOLVED] how to ..."). This will make it easier for the community to follow the posts yet to be attended.
Re: ProbABEL: Which allele is the effective allele?
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
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
Re: ProbABEL: Which allele is the effective allele?
wuttke wrote: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.
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Lennart Karssen
PolyOmica
The Netherlands
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Lennart Karssen
PolyOmica
The Netherlands
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