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.

Rx