We calculate statistics S(x) for each possible value of gcp=x, using equation (2). These statistics also depend on the heritability[19], the genetic correlation[16], and the cross-trait LDSC intercept[19]. We estimate the variance of these statistics using a block jackknife and obtain an approximate likelihood function for the gcp. We compute a posterior mean gcp estimate (and a posterior standard deviation) using a uniform prior. We test the null hypothesis (that gcp=0) using S(0). Details of the method are provided in the Methods section. We have released open source software implementing the LCV method (see URLs).
