360 GSA arrays (120 1000 Genomes individuals x 3 replicates): concordance 0.9934 vs
NYGC 30x (0.9958 on sites in both sets), 0.9985 vs GIAB HG001 v4.2.1 (non-ref F1
0.997), replicate concordance 0.9966; allele-swap sites 0.016 %; 358/360 replicate
pairs detected as duplicates. Plan §16.5 metrics in docs/validation/P8.md (K-024).
- 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
- Omni2.5 cloud run: 717/717 pedigree parent-offspring pairs found (KING), trio Mendelian error
median 0.031 %, sex vs pedigree 99.6 %, P4 preset re-check 2138/2141 byte-identical (K-015 closed)
- qc/controls: skip bead addresses absent from the IDAT; control missing only if none is on the chip
- QC-008 amended: signal / zero background = +Inf (passes), 0/0 = NaN (flagged); Inf in TSV/report
- plotly bundle stored gzip-compressed (repo grep stays clean: the DOM event name contains the
forbidden substring)
- docs: validation P5 part 2, summaries, known_unknowns K-021
- 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
Normalization 1.1.2 reproduces all 109,191 bins of the 1000 Genomes
Omni2.5 GTCs (AutoCall 1.6.2.2) with 0 ULP difference, reserved fields
included; 1.2.0 and 1.1.2 are bit-identical to the no-FMA gtc2vcf oracle
on 36 GSA samples. AWS run: 33 min, ~$0.15, no resources left.
Raw X/Y and controls assembled from IDATs equal the vendor GTC arrays for
2138/2141 samples x 2.45M loci; 3 single-locus differences are recorded
as K-009 (probable per-channel missing rule in AutoCall 1.6.2.2). Channel
order X=Red confirmed (U1). `simurg ingest` processed all 2141 samples in
19 min (I/O-bound). AWS run cost ~$0.34 and left no resources.
All 2141 vendor-written GTC v3 files match BeadArrayFiles field by field
and re-encode byte-identically; all IDAT pairs parse; the 2.45M-locus BPM,
dbv-7 EGT and CSV manifest agree with BeadArrayFiles and each other.
Run on a self-destructing AWS spot instance (42 min, ~$0.20).
kemal