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heritability-partitioning

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Estimates SNP heritability and partitions it across functional annotations, cell types, and loci from GWAS summary statistics or individual-level genotypes. Implements LDSC, stratified LDSC with the baseline-LD model, Finucane 2018 cell-type prioritization, LDAK SumHer, HDL, HESS local heritability, BOLT-REML, GCTA-GREML, graphREML, and Popcorn cross-population genetic correlation. Use when computing total h2_SNP from summary stats, partitioning heritability across functional categories, prioritizing trait-relevant tissues or cell types from ENCODE/Roadmap chromatin marks, reconciling LDSC vs LDAK enrichment estimates, computing local heritability with HESS, estimating genetic correlation between traits, or producing publication-grade enrichment with calibrated sensitivity to model assumptions.

When to use

• computing total h2_SNP from summary stats
• partitioning heritability across functional categories
• prioritizing trait-relevant tissues or cell types
• reconciling LDSC vs LDAK enrichment estimates
• computing local heritability with HESS
• estimating genetic correlation between traits
• producing publication-grade enrichment

When not to use

• non-EUR ancestry with EUR LD scores
• sample size too low (mean chi-square < 1.02)
• population stratification not captured
• sample overlap > 5% for HDL
• non-EUR HDL eigen-reference

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