P6 validated against GTCtoVCF too: zero unexplained genotype differences

- GTCtoVCF (Apache-2.0, 36 GSA samples, merged sites): 23.66 M identical calls; every difference named
  (intensity-only probes merged by the oracle, its opposite-strand indel bug EDGE-012, normalisation-based
  grouping, OUT-018 ploidy); indel representations identical, including 144 gtc2vcf cannot resolve
- validate_p6_vcf.py: rule-based categories (--bpm for [I/D]/[D/I] detection)
- docs: validation P6 complete, README status

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

README.md

@@ -16,8 +16,13 @@ Phase **P5 (QC)** is complete: control-probe metrics, thresholds/profiles, two-a
 KING-robust relatedness, Mendelian errors, locus summary and a self-contained HTML report (`simurg qc report`). On 2141
 1000 Genomes samples all 717 pedigree parent–offspring pairs are recovered and trio Mendelian error rates are ~0.03 %
 (`docs/validation/P5.md`).
+Phase **P6 (outputs)** is complete: `simurg gtc-to-vcf` (plus-strand harmonisation with audit, merged multi-probe
+sites, per-sample VCF.gz + tabix or a cohort BCF + CSI) and `simurg export plink|bedgraph|finalreport|locus-summary`.
+On the GSA demo, genotypes match gtc2vcf and GTCtoVCF with zero unexplained differences and PLINK files match plink2
+(`docs/validation/P6.md`).
 Available commands: `simurg version`, `simurg inspect <files…> [--json]`, `simurg ingest`, `simurg normalize`, `simurg genotype`,
-`simurg qc controls|samples|contamination|relatedness|loci|report|suggest-thresholds`.
+`simurg qc controls|samples|contamination|relatedness|loci|report|suggest-thresholds`, `simurg gtc-to-vcf`,
+`simurg export plink|bedgraph|finalreport|locus-summary`.
 
 ## Quick start
 
@@ -28,6 +33,8 @@ bash scripts/bootstrap_refs.sh            # reference open-source repos → refs
 bash scripts/fetch_data.sh p0             # ~1.4 GB of public test data → data/
 bash scripts/make_oracle_gtcs.sh          # builds gtc2vcf, writes oracle GTCs
 bash scripts/make_oracle_qc.sh            # locus-summary oracle (BeadArrayFiles, separate venv)
+bash scripts/fetch_data.sh p6             # GRCh38 FASTA (~0.9 GB download, 3.1 GB unpacked)
+bash scripts/make_oracle_vcf.sh           # gtc2vcf oracle VCF for the P6 tests
 uv run pytest tests/oracle                # real-data acceptance tests (add -m "not slow" to skip the long ones)
 uv run simurg inspect data/p0/gsa_v4_pgx/idats_Demo_36/idats_Demo_36/207895980019/207895980019_R03C01_Grn.idat
 ```