Synthetic cohort¶

The generator examples/generate_cohort.py writes VCF, PGEN, and PLINK1 files for hg38, hg19, and CHM13.

pip install -e .
python examples/generate_cohort.py
./examples/run_synthetic.sh

./examples/run_synthetic.sh runs the hg38 VCF, PGEN, and PLINK1 files.

Expected calls (two-marker, --assume-trans) are listed in examples/data/expected_calls.txt.

S06_seSew is the unphased double-het: weak-secretor by default, ambiguous with --no-assume-trans. Phased VCFs encode that sample as trans (0|1 at both markers).

Example report¶

Snapshot of PREFIX.report.html from the hg38 VCF (--method two-marker). Research demo, not clinical typing.

Open full report — 14-sample two-marker demo (determined calls and missing markers).