Quality control of per-study summary statistics included evaluation and correction of strand flips and allele flips through systematic comparison of alleles and allele frequencies against the reference datasets ExAC v2.0, 1000 Genomes Phase 3, and dbSNP. Variants with call rates<0.9, or Hardy Weinberg p<1×10−7 were also removed. The latter filter was meant to avoid findings that could not be more broadly replicated across the 17 studies.
