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Welcome to the MAGGIE wiki, which is also the main source of documentation!

If you're just starting to use LD Score, the tutorials on LD Scores; heritability, genetic correlation and the LD Score regression intercept; and partitioned h2 describe how to run ldsc. The FAQ answers several common questions.

Note: Summary statistics from linear mixed models cannot be used to estimate SNP-heritability, but they can be used for estimating genetic correlation and partitioned heritability. This is because they have an "effective sample size" which differs from the true sample size; this affects SNP-heritability estimates but cancels out in the estimation of genetic correlation or proportion of heritability.