PLINK output (.assoc) files were modified with columns for direction of association, sample size, and strand. For most samples, sample size equaled the sum of cases and controls included in the final analysis, after quality control. For the STEP-BD sample, sample size was set to equal the number of cases only. This was done to avoid over-weighting the results from the NIMH control sample, largely overlapping portions of which were included in both the NIMH bipolar disorder and STEP-BD samples. Modified files were loaded into Metal (July, 2008 version), then processed using the GENOMICCONTROL option, which applies a genomic control22 correction in samples where the genomic inflation factor is greater than 1.0. Metal weights each sample based on the square root of the sample size.
