P6 complete: optional VCF fields, SNV+indel merging, auxiliary MNV loci, PLINK 2 .pgen

- gtc-to-vcf --info-fields ASSAY_TYPE,NORM_BIN,GENTRAIN,CLUSTER_SEP,ILMN_STRAND,PROBE_IDS (--egt) and
  --extra-format X,Y,NORMX,NORMY,THETA,R, in per-sample VCFs and the --merge BCF (OUT-012, plan §8.3);
  equal to gtc2vcf's values (THETA/R missing where both normalized intensities are 0, K-023)
- --merge-snv-indel (OUT-021, EDGE-013): alleles extended to the longest REF; SNV probes read the base at POS
- --auxiliary-loci (OUT-035, EDGE-015): rules (a)-(e), E_AUX_INVALID; rule (d) uses the last plus-strand base
  for minus-strand designs (spec amended, as GTCtoVCF)
- export plink --format bed|pgen|both: PLINK 2 fixed-width .pgen/.pvar/.psam; plink2 reads it back to a .bed
  byte-identical to ours
- cohort store keeps raw/normalized intensities for the BCF path; tests (unit + gtc2vcf oracle); docs

docs/validation/P6.md

@@ -74,10 +74,16 @@ has the dash on the right (patched to skip instead of crash), which SimurgArray
   (float32), otherwise unchanged (> 500 sites of each kind checked per sample).
 * EDGE-023: raw LRR bedGraph values equal the GTC values after `%.6g` formatting for every single-probe position.
 
-### Not yet implemented (listed in known_unknowns K-023)
+### Optional outputs (completed 2026-09-28)
 
-`--auxiliary-loci` (OUT-035), `--info-fields` and `--extra-format` (OUT-012), `--merge-snv-indel` (OUT-021),
-PLINK 2 `.pgen` output.
+| Option | Check | Result |
+|---|---|---|
+| `--info-fields ASSAY_TYPE,NORM_BIN,GENTRAIN,CLUSTER_SEP,ILMN_STRAND,PROBE_IDS` (`--egt` for the cluster scores) | INFO vs gtc2vcf `ASSAY_TYPE`, `GenTrain_Score`, `Cluster_Sep`, 3 samples | identical |
+| `--extra-format X,Y,NORMX,NORMY,THETA,R` | vs gtc2vcf FORMAT tags, 1 965 810 probe × sample values | X, Y, NORMX, NORMY identical (within the 6-digit print of `bcftools query`); THETA/R identical except 148 values where both normalized intensities are 0: missing for SimurgArray (plan §7.4, as the caller sees them), 0 for gtc2vcf |
+| both, in `--merge` BCF | BCF vs per-sample VCFs, 1 970 064 records × all fields | 0 differences |
+| `--merge-snv-indel` (OUT-021, EDGE-013) | 1 GSA sample; `bcftools norm -c e -f` | 677 SNV+indel positions merged (635 796 → 635 119 records), 0 REF mismatches; unit test of the combined genotypes |
+| `--auxiliary-loci` (OUT-035, EDGE-015) | unit tests for every rule (a)–(e) and a minus-strand design; 3 real probes (plus and minus designs) redefined as MNVs | records replaced, genotypes preserved, 0 REF mismatches |
+| `export plink --format pgen|both` (plan §8.4) | `plink2 --pfile` on our `.pgen` → `.bed` | byte-identical to our own `.bed` (637 397 variants), no plink2 warnings |
 
 The example rows in `P6_gsa36_vs_gtc2vcf.json` and `P6_gsa36_vs_gtctovcf.json` show probe names as stable
 pseudonyms (`locus_NNNN`); sample IDs, positions, alleles and all counts are the original values.