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bio-population-genetics-linkage-disequilibrium

Maintainer FreedomIntelligence · Last updated April 1, 2026

Compute LD metrics (r², D') and LD decay analysis.

OpenClawNanoClawAnalysisReproductionbio-population-genetics-linkage-disequilibrium🧠 bioos extended suitebioos extended bioinformatics suitecompute

Original source

FreedomIntelligence/OpenClaw-Medical-Skills

https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/bio-population-genetics-linkage-disequilibrium

Maintainer
FreedomIntelligence
License
MIT
Last updated
April 1, 2026

Skill Snapshot

Key Details From SKILL.md

2 min

Key Notes

  • Calculate LD statistics, prune correlated variants, and identify haplotype blocks.
  • plink2 --bfile data --r2 --ld-window-kb 1000 --ld-window-r2 0.2 --out ld_results.

Source Doc

Excerpt From SKILL.md

With SNP names in output

plink2 --bfile data --r2 inter-chr --ld-window-r2 0 --out all_pairs

Squared correlation matrix

plink2 --bfile data --r2-phased square --out ld_matrix


## ld_results.ld contains:

CHR_A  BP_A  SNP_A  CHR_B  BP_B  SNP_B  R2

Use cases

  • Use bio-population-genetics-linkage-disequilibrium for genomics and bioinformatics workflows.
  • Apply bio-population-genetics-linkage-disequilibrium to sequencing, variant, or omics analysis tasks.

Not for

  • Do not rely on this catalog entry alone for installation or maintenance details.

Upstream Related Skills

  • plink-basics - File format handling
  • population-structure - Use pruned data for PCA
  • association-testing - LD clumping for GWAS
  • selection-statistics - LD affects EHH statistics

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