bio-causal-genomics-heritability-partitioning

Name: bio-causal-genomics-heritability-partitioning
Rating: 5 (1 reviews)
Author: bg-szy

Estimate SNP heritability and partition 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 computin

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Updated 14 days ago

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Version Compatibility

Reference examples tested with: LDSC v1.0.1+ (Python 3 fork; prefer abdenlab/ldsc-python3 v2.0.0 which retains the working --h2 / --rg / --h2-cts CLI -- belowlab/ldsc v3.0.1 explicitly broke that CLI per its README and is best run via Docker jtb114/ldsc:latest), LDAK 6.0+, BOLT-LMM 2.4.1+, GCTA 1.94+, HESS 0.5.4+, HDL 1.4.0+ (R; GitHub zhenin/HDL), Popcorn 1.0+ (Python; brielin/Popcorn), baselineLD_v2.2 annotations (alkesgroup.broadinstitute.org/LDSCORE).

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