To estimate SNP heritability (h2g) and genetic correlation (rg), we used the software and protocol from the Bulik-Sullivan et al. study (2015a) (http://www.github.com/bulik/ldsc) and applied it to our datasets. To control for imputation quality, only those SNPs found in HapMap3 with a 1000 Genomes EUR MAF>0.01 were included (integrated_phase1_v3.20101123). Next, insertions and deletions (indels) and structural variants were removed along with strand-ambiguous SNPs. LD scores and weights were downloaded from the Broad institute (http://www.broadinstitute.org/~bulik/eur_ldscores/). An unconstrained intercept was used in the regression model. The code created for this study is available at https://github.com/achorton/LDSC_for_Hartz_et_al.
