File S4 is organized as five notebooks. The first prepares the
per-chromosome LD matrices, the next three run LDna on each chromosome, and
the last combines the Single-Outlier Cluster (SOC) results genome-wide.
File S4 — five parts
S4a
LDna data preparation
Per-chromosome LD matrix construction from the filtered SNP chip genotypes, ready for LDna.
View notebook →
S4e
Combined LDna results
Genome-wide summary of Single-Outlier Clusters across chromosomes 1–3.
View notebook →
Method. All five notebooks run in the project container
ghcr.io/cosmelab/aealbo_autogeny:latest and use the
LDna
package (v2.15, Kemppainen et al. 2015). The CLI pipeline equivalent is
scripts/05_ldna/run_ldna.sh in the repository.