Keeping both A1/A2 in PLINK for assoc/logistic output

Question

[gradstudentNew]

Hey guys,

I was wondering if there's anyway to keep both A1 and A2 in PLINK for the logistic output? I used to merge my freq. output and assoc output. However, since I use HWE / MAF filters, it only applies to the logistic and the merging no longer works since they're not in order anymore.

Any suggestions? Thank you all!

Answer 1

[Kevin Blighe]

Plink automatically sets A2 as the major allele and then tests A1 (minor allele) for the purposes of regression. You could switch these through the use of the --a1-allele / --a2-allele flags.

Kevin

Answer 2

[chrchang523]

Use plink 2.0 --glm for this; it gives you a lot more flexibility re: what columns are included in the output, and by default both alleles are shown (and there's a third column indicating which allele is currently being regressed on).