Examples¶

Example cohorts live under examples/.

Research use only

These examples are for software demos, not clinical typing.

Unit-test fixtures under tests/fixtures/synthetic/ remain a separate clean 6-sample set.

Prerequisites¶

# from repository root
pip install -e .
python examples/generate_cohort.py

./examples/run_all.sh

Outputs land in examples/out/ (TSV + HTML run report).

Page	What it covers
Synthetic cohort	Formats (VCF, PGEN, PLINK1), builds (hg19/hg38/chm13), phased VCF, marker notations
1000 Genomes FUT2 slices	EAS / EUR / AFR tag-SNP extracts, `--phase auto` vs `--phase unphased`
1000 Genomes `--assume-trans`	Phased AFR/AMR/EAS/EUR vs unphased `--assume-trans` (cis/trans, not serology)
Marker LD r²	Pairwise haplotype r² for the three tag SNPs in AFR/AMR/EAS/EUR
Example reports	Committed HTML snapshots (1KG EAS / EUR / AFR and synthetic)

Regenerate the committed HTML reports after changing the report renderer:

./examples/export_docs_reports.sh