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kemal 5d3e334ab7 P4 validated on 2141 vendor GTCs; legacy AutoCall 1.6.2 preset

- vendor comparison (1000 Genomes Omni2.5, AutoCall 1.6.2.2): every
  computed field identical in 2138/2141 samples; the 3 others trace back
  to the single-locus raw-intensity rule (K-009); sex rule 1 matches all
- AutoCall 1.6.2.x leaves GC10/GC50/#calls/#no-calls at 0 in GTC v3:
  new `--preset autocall-1.6.2` (1.1.2 normalization, sex rule 1, GTC v3,
  legacy statistics); the sample summary keeps the real statistics
- NaN sign canonicalised to the x86 pattern (K-014); report P4.md

2026-09-28 01:21:49 +01:00

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Phase P4 validation report — genotype calling and GTC output

Date: 2026-09-28. Development and oracle tests on the Pi; vendor comparison on a self-destructing AWS spot instance (run-20260927T233126Z, 44 min, ≈ $0.19). Summary: P4_omni2141_summary.json.

Delivered

Item	Module
Cluster file aligned to manifest order (float32 mean R)	`genotype/clusters.py`
GenCall-equivalent calling: SD flair, six-case half-flattened likelihoods, priors/posteriors, fuzzy sub-scores, score map	`genotype/gencall.py`
BAF / LRR / LogR dev (Peiffer 2006), canonical NaN pattern	`genotype/baf_lrr.py`
Sex estimate, rules v1 and v2	`genotype/sex.py`
IDAT pair → complete GTC (v5 or v3), TOP-strand base calls, sample stats, presets	`genotype/sample.py`
`simurg genotype` (GTC per sample, `sample_summary.tsv/json` per OUT-060…063, run manifest)	`pipeline/genotype.py`

Acceptance (plan §18 P4)

Against the oracle (gtc2vcf built without FMA), P0 GSA data

Check	Result
36 samples × normalization 1.2.0 and 1.1.2: whole GTC files after aligning the four free-text fields (file names, AutoCall date/version)	72/72 byte-identical

Every data field matches bit for bit: raw X/Y, transforms, genotypes, GenCall scores, TOP base calls, BAF, LRR, call rate, sex, LogR dev, GC10/GC50, call counts, percentiles and controls. The only adjustment is the sign of NaNs that libm computes (K-014).

Against 2141 vendor GTCs (1000 Genomes Omni2.5, AutoCall 1.6.2.2, cluster file `HumanOmni2.5-4v1-Multi_B.egt`)

Field	Samples that differ	Explanation
genotypes	3 (5 loci in total)	the 3 samples of K-009, whose raw intensity differs in one locus; that difference shifts their normalization
GenCall scores	3 (18 229 loci)	same 3 samples (the transform change moves every score of the affected bin)
normalization transforms	2	same K-009 samples
raw X / raw Y	1 / 2	K-009
call rate, LogR dev	2 / 3	follow from the above
base calls	3	follow from genotypes
sex (rule 1)	0 of 2141	rule 2 would differ in 12 samples, so AutoCall 1.6.2.2 uses rule 1
GC10, GC50, #calls, #no-calls	2141	AutoCall 1.6.2.2 leaves these at 0 in GTC v3 (K-015); now emulated by `--preset autocall-1.6.2`

So in 2138 of 2141 samples every computed field agrees with the vendor; the remaining 3 samples trace back to the single-locus raw-intensity rule of K-009. Whole-file byte identity was 0/2141 in this run only because of the four legacy-empty statistics; the preset that reproduces them was added after the run (unit-tested, not yet re-run on the cloud — expected 2138/2141).

Not covered here: BAF and LRR against vendor output (GTC v3 has no BAF/LRR fields). The 1000 Genomes Sanger set ships a GenomeStudio Final Report with BAF/LRR for 177 samples — optional follow-up run (≈ $0.10).

Performance

Machine	Result
Raspberry Pi 5, GSA (683 k loci)	3.6 s per sample (1 core); 36 samples in 2 min with 4 workers
AWS m7g.4xlarge, Omni2.5 (2.45 M loci), 16 workers	2141 samples genotyped and compared in 19.6 min; peak RSS 3.2 GB

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