# Expected under: genoabo DATA --build <build> --method three-marker
# Unphased files use --assume-bo by default (S04_BO → B). --no-assume-bo leaves S04 ambiguous.
# Phenotypes are build-independent; coordinates differ by build directory.
IID	scenario	expected_group	expected_qc	notes
S01_AA	determined	A	PASS	classic A/A
S02_AO	determined	A	PASS	classic A/O
S03_BB	determined	B	PASS	classic B/B
S04_BO	determined	B	PASS	classic B/O (--assume-bo default; ambiguous with --no-assume-bo)
S05_AB	determined	AB	PASS	classic A/B
S06_OO	determined	O	PASS	classic O/O
S07_AA_dup	determined	A	PASS	duplicate A/A
S08_OO_dup	determined	O	PASS	duplicate O/O
S09_missO	missing	NA	MISSING_MARKER	rs8176719 missing
S10_missAB6	missing	NA	MISSING_MARKER	rs8176746 missing
S11_missAB7	missing	NA	MISSING_MARKER	rs8176747 missing (three-marker)
S12_missAll	missing	NA	MISSING_MARKER	all markers missing
S13_missO_proxy	missing	NA	MISSING_MARKER	miss O; proxy present but unused by three-marker
S14_missProxy	determined	O	PASS	miss rs505922 only; still O/O
S15_conflictB	undetermined	NA	CONFLICT	6746 B vs 6747 A conflict
S16_conflictB_rev	undetermined	NA	CONFLICT	6746 A vs 6747 B conflict
S17_missRequired	missing	NA	MISSING_MARKER	miss both rs8176719 and rs8176746
S18_hetO_missAB	missing	NA	MISSING_MARKER	het O; miss both B markers

# Tallies (three-marker, --assume-bo default): A×3, B×2, AB×1, O×3; undetermined/missing ≈ 9
# --no-assume-bo: S04_BO ambiguous; A×3, B×1, AB×1, O×3

# Phased VCFs (cohort_phased.vcf): S04_BO is B from cis/trans; other determined phenotypes match.
# Use --phase auto|phased; phase_mode=phased; confidence often high for determined calls.
# Heterozygotes use 0|1 (alt on haplotype 2). Homozygotes 0|0 / 1|1. Missing ./.
