PGx validation on GSE165845: WGS-derived star truth, 2-fold masks, array-resolvable concordance

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- scripts/pgx/wgs_star_truth.py: star alleles from the 1000G 30x phased panel with the DB definitions
  (wildcard-aware haplotype assignment; checked against GeT-RM on the demo CEPH individuals).
- validate_star_getrm.py: --all-genes, --individuals, --coverage (projection onto what the array can see);
  replicate_concordance.py.
- 120 individuals x 3 GSA v1 arrays: array-resolvable 1637/1710 (95.7 %), top 1223/1800 (chip lacks many
  defining variants), GeT-RM subset 28/35, replicates 99.2 % without the failed array (V2_pgx_star.md, K-029).

Co-Authored-By: Claude Opus 5.5 <[email protected]>
Claude-Session: https://claude.ai/code/session_01814GKVzZVL3FuF3DeiZXhv

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kemalandClaude Opus 5.5 committed 2026-09-29 19:00:34 +01:00

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docs/validation/V2_pgx_star_gse165845.json

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