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Quick Start

Run the smoke test

Run the smallest scenario to confirm the pipeline is functional (this takes a minute or two):

snakemake --cores 4 results/test/small_test/scenario.done

Check the output

ls results/test/small_test/rep1/    # pedigree.parquet, phenotype files, validation, stats
cat logs/test/small_test/rep1/simulate.log

A successful run produces these key files per replicate:

File What it contains
pedigree.parquet Full pedigree with parent links, generation, sex, liability components
phenotype.parquet Censored time-to-event phenotypes (age-at-onset, affected status)
phenotype.simple_ltm.parquet Liability-threshold binary affected status
validation.yaml Structural and statistical validation results
phenotype_stats.yaml Phenotype statistics (correlations, prevalence, CIF)
params.yaml The resolved parameters for this replicate

Explore the atlas

Per-scenario plots are compiled into a multi-page PDF atlas:

results/test/small_test/plots/atlas.pdf

See Interpreting Results for descriptions of each plot.

Next steps