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Note that the LD scores will be used in the LD score regression analysis to estimate the SNP-based heritability for a trait based on summary data, genetic correlation between two traits, and to estimate the degree of overlap between two samples (see Zhu et al. 2018 Nat. Commun.
These flags include --clump-p1, --clump-r2, --gwas-thresh, --heidi-thresh, --heidi-snp, --gsmr-snp and --gsmr-ld-fdr. Previous data management options such as --keep, --extract and --maf, REML analysis options such as --reml-priors, --reml-maxit and --reml-no-constrain and multi-threading option --thread-num are still valid for this analysis.