kemalandClaude Opus 5.5
0fe3977187
- 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
81 lines
5.2 KiB
Markdown
81 lines
5.2 KiB
Markdown
# Phase P6 validation — outputs (VCF/BCF, PLINK, bedGraph, final report)
|
||
|
||
Date: 2026-09-28. All work on the Raspberry Pi (no cloud cost). Data: the 36 GSA v4 PGx oracle GTCs (P4, byte-identical
|
||
to gtc2vcf's), the GSA BPM + CSV manifest, and the Ensembl GRCh38 primary assembly (release 110, `fetch_data.sh p6`).
|
||
|
||
## Delivered
|
||
|
||
| Item | Module |
|
||
|---|---|
|
||
| FASTA access: plain/BGZF, `.fai`/`.gzi` read and built (identical to htslib's), index check, build detection, contig aliases, mmap genome cache | `formats/fasta.py` |
|
||
| BGZF writer, tabix `.tbi`, BCF 2.2 encoder, CSI index (pure Python) | `formats/bgzf.py`, `formats/bcf.py` |
|
||
| Plus-strand mapping with audit row per locus; indel resolution from `SourceSeq` (context score), left normalisation | `harmonize/sites.py` |
|
||
| Site grouping and the OUT-031 genotype-combination algorithm (ploidy-aware, Infinium I/II signal classes) | `harmonize/combine.py` |
|
||
| `simurg gtc-to-vcf` (per-sample VCF.gz + .tbi, `--merge` cohort BCF + .csi, audit Parquet) | `pipeline/vcf.py` |
|
||
| `simurg export bedgraph | finalreport | plink | locus-summary` | `pipeline/export.py` |
|
||
|
||
## Acceptance (plan §18 P6)
|
||
|
||
### bcftools validation and indexes
|
||
|
||
Every VCF passes `bcftools view`; `bcftools index --nrecords` on our `.tbi` equals the record count (635 796); region
|
||
queries through our index (`1:1-2M`, `X:150-156M`, `MT`, `Y`, `22:30.0-30.1M`) return exactly the records a full scan
|
||
finds. The cohort BCF reads back identically to the per-sample VCFs (635 796 records × 3 samples, 0 differences in
|
||
GT/GS/BAF/LRR) and its CSI index answers region queries.
|
||
|
||
### Genotypes vs gtc2vcf (MIT), 36 samples, one record per probe (`--unsquash-duplicates`)
|
||
|
||
Both sides left-aligned with `bcftools norm -f`, compared per probe and sample as allele sets.
|
||
|
||
| Category | Count (probe × sample) | Explanation |
|
||
|---|---|---|
|
||
| identical calls | 23 656 010 | |
|
||
| identical no-calls | 102 077 | |
|
||
| `grouping_differs` | 6 424 | the probe belongs to a SimurgArray multi-allelic site (kept merged even with `--unsquash-duplicates`, OUT-034); the site genotype uses every probe (e.g. an Infinium II [G/T] probe calls GG while the site is G/C: C shares G's dye) or is missing when the probes contradict each other |
|
||
| `ours_missing_het_in_haploid` | 16 | male X non-PAR and MT heterozygous calls → missing (OUT-018) |
|
||
| `ours_missing_haploid_Y` | 9 | Y of female samples → missing (OUT-018) |
|
||
| `representation_diff` | 5 184 (144 probes) | indels gtc2vcf leaves unresolved (`REF=I/D`); our representation agrees with GTCtoVCF (below) |
|
||
| **unexplained** | **0** | |
|
||
|
||
Summary: `P6_gsa36_vs_gtc2vcf.json`.
|
||
|
||
Locus sets: gtc2vcf writes 22 400 intensity-only loci that SimurgArray skips by design (OUT-019), and 49 indels it
|
||
cannot resolve either (`W_SKIP_INDEL_REF` for us). Nothing we write is missing from gtc2vcf.
|
||
|
||
### Genotypes vs GTCtoVCF (Apache-2.0), 36 samples, merged sites (default squashing)
|
||
|
||
GTCtoVCF 1.2.1 run under Python 3 with two local compatibility patches (K-022), alt-contig loci filtered.
|
||
|
||
| Category | Count (probe × sample) | Explanation |
|
||
|---|---|---|
|
||
| identical calls | 23 656 575 | |
|
||
| identical no-calls | 109 760 | |
|
||
| `oracle_site_includes_probes_we_skip` | 2 917 | GTCtoVCF merges intensity-only CNV probes (e.g. `ilmnseq_CYP2C8_…_CNV`) into SNV sites; their alleles make its call ambiguous. SimurgArray skips intensity-only loci (OUT-019) |
|
||
| `oracle_opposite_strand_indel_bug` | 177 | `[I/D]` and `[D/I]` duplicate indel probes all heterozygous: we write `0/1`, GTCtoVCF 1.2.1 `./.` — the reference bug named in OUT-020/EDGE-012 |
|
||
| `grouping_differs` | 155 | indel probes designed 1–3 bp apart normalise to the same variant: we merge them (OUT-030), GTCtoVCF groups by manifest position; the probes disagree, so the merged site is missing |
|
||
| `ours_missing_het_in_haploid` | 17 | OUT-018 |
|
||
| `ours_missing_haploid_Y` | 9 | OUT-018 |
|
||
| `oracle_diploid_candidates_in_haploid_context` | 2 | tri-allelic male-X site: we enumerate haploid candidates (OUT-031 step 3) and get one call; GTCtoVCF always enumerates diploid ones |
|
||
| representation differences | 0 | every indel (including the 144 gtc2vcf cannot resolve) is written identically after left-alignment |
|
||
| **unexplained** | **0** | |
|
||
|
||
Probe sets: GTCtoVCF also writes the 22 400 intensity-only loci; it drops the 3 CYP2D6 indels whose `SourceSeq`
|
||
has the dash on the right (patched to skip instead of crash), which SimurgArray writes. Summary:
|
||
`P6_gsa36_vs_gtctovcf.json`.
|
||
|
||
### PLINK vs plink2 (GPL, subprocess oracle, built from source)
|
||
|
||
`simurg export plink` and `plink2 --bcf <bcftools norm -m- of our BCF> --make-bed --split-par hg38` agree on all
|
||
637 397 variants × 3 samples (bed codes identical; the 1 601 extra variants are split multi-allelic sites).
|
||
|
||
### BAF orientation, bedGraph
|
||
|
||
* EDGE-017: at every called homozygous single-probe site where the probe's A allele is ALT, VCF BAF = 1 − GTC BAF
|
||
(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)
|
||
|
||
`--auxiliary-loci` (OUT-035), `--info-fields` and `--extra-format` (OUT-012), `--merge-snv-indel` (OUT-021),
|
||
PLINK 2 `.pgen` output.
|