Summary statistics for SNPs in LD are correlated, so the OLS standard error will be biased downwards. We estimate a heteroskedasticity-and-correlation-robust standard error with a block jackknife over blocks of adjacent SNPs. This is the same procedure used in [19], and gives accurate standard errors in simulations (Table 1). We obtain a standard error for the genetic correlation by using a ratio block jackknife over SNPs. The default setting in ldsc is 200 blocks per genome, which can be adjusted with the -num-blocks flag.
