Using PLINK to do meta-analysis, one uses the form
plink --meta-analysis study1.assoc study2.assoc study3.assoc
But in doing so, if there is a mismatch among alleles from the files you are feeding in (study1.assoc, study2.assoc, etc.), the studies won't be incorporated and the plink.prob file output will give the error "ALLELE_MISMATCH". The problem is that the output going in comes from logistic regression files where the reference allele is the minor allele--which often varies between populations. Is there a way to carry out logistic regression in PLINK while keeping the reference allele constant between studies? Alternately, is there a way to alter the output of the study.assoc files so they contain both alleles so that PLINK can perform meta-analysis. In the present logistic output, they look like so.
study1.assoc CHR SNP BP A1 TEST NMISS OR SE L95 U95 STAT P 1 rs17556883 38969651 C ADD 1150 1.101 0.08288 0.9361 1.295 1.163 0.2449 study2.assoc CHR SNP BP A1 TEST NMISS OR SE L95 U95 STAT P 1 rs17556883 38969651 T ADD 1150 1.101 0.08288 0.9361 1.295 1.163 0.2449
Above, notice the A1 is C for study 1 and T for study 2. Therein lies the problem.
Thanks for any help.