Setting the ALT allele as the A1 allele

[Marta R.]

Hello! 

I am trying to run a regression on a dataset I have, and I believe plink2 automatically uses the minor allele as the A1 allele, which may not always be the ALT allele. In my analysis, I need to have the ALT allele as the A1 allele even if it's the major one. 

I have seen that in plink1.9 there's the function --a1--allele which if I'm not mistaken can force the ALT allele to become the A1 allele; and I have seen functions for plink2.0 like --omit-ref, but I'm not sure it would have the same result after reading the documentation.

Can anyone confirm that adding omit-ref would force for all the beta effects to be based on the ALT allele even if it's the major allele? Is there any downside or consideration when using --omit-ref?

Thank you so much!

M

[Chris Chang]

Yes, the 'omit-ref' modifier to --glm (note that it isn't a separate flag, "--omit-ref" won't work) causes --glm's beta effects to be calculated for the ALT allele.

The known downside relates to interaction testing; if you are not using the 'interaction' --glm modifier, you don't have to worry about it.

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