Second, for each trait, we restrict variation in SNP sample sizes by calculating the 90th percentile of the SNP sample-size distribution and removing SNPs with a sample size smaller than 75% of this value. This filter is similar to, though slightly more strict than, the sample-size filter recommended for LD Score regression.14 If a SNP’s effect is estimated in a relatively small subset of the sample, then the sample overlap across traits will likely be different for that SNP than for other SNPs in the sample. In that case, the covariance of the estimation error across traits as estimated by LD score regression may not be a good approximation to the covariance of the estimation error for that particular SNP.
