We used RPS 14 as an alternative and complementary way to compare the overall patterns of results from the PGC schizophrenia analysis (discovery sample) with the independent Swedish results (target sample). We began by selecting a high-quality, relatively independent SNPs with unambiguous directions of effects: from the PGC imputed results file, we made a subset of results containing SNPs with allele frequency 0.02-0.98 and imputation INFO scores > 0.9. We then removed SNPs in high LD using via clumping (i.e., retain all SNPs with r2< 0.25 within 500 kb windows):
