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SimurgArray/docs/validation/P6_gsa36_vs_gtctovcf.json
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kemal d3add008f7 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
2026-09-28 13:20:44 +01:00

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"22216499",
"A",
"T"
]
],
[
"207895980035_R05C03",
"locus_0083",
[
"X",
"7462384",
"A",
"G",
"."
],
"0/1",
[
"X",
"7462384",
"A",
"G"
]
],
[
"207895980035_R05C03",
"locus_0084",
[
"X",
"7475195",
"T",
"C",
"."
],
"0/1",
[
"X",
"7475195",
"T",
"C"
]
],
[
"207895980035_R05C03",
"locus_0072",
[
"X",
"68391913",
"C",
"T",
"."
],
"0/1",
[
"X",
"68391913",
"C",
"T"
]
],
[
"207895980035_R09C03",
"locus_0074",
[
"MT",
"2690",
"G",
"A",
"."
],
"0/1",
[
"MT",
"2690",
"G",
"A"
]
],
[
"207895980035_R11C03",
"locus_0080",
[
"X",
"91616889",
"G",
"A",
"."
],
"0/1",
[
"X",
"91616889",
"G",
"A"
]
],
[
"207895980035_R12C03",
"locus_0079",
[
"X",
"20830034",
"A",
"G",
"."
],
"0/1",
[
"X",
"20830034",
"A",
"G"
]
],
[
"207895980035_R13C03",
"locus_0070",
[
"X",
"7467632",
"A",
"G",
"."
],
"0/1",
[
"X",
"7467632",
"A",
"G"
]
],
[
"207895980035_R13C03",
"locus_0124",
[
"X",
"7478861",
"T",
"C",
"."
],
"0/1",
[
"X",
"7478861",
"T",
"C"
]
],
[
"207895980035_R13C03",
"locus_0071",
[
"X",
"7478861",
"T",
"C",
"."
],
"0/1",
[
"X",
"7478861",
"T",
"C"
]
],
[
"207895980035_R13C03",
"locus_0072",
[
"X",
"68391913",
"C",
"T",
"."
],
"0/1",
[
"X",
"68391913",
"C",
"T"
]
],
[
"207895980035_R14C01",
"locus_0076",
[
"X",
"120442599",
"C",
"T",
"."
],
"0/1",
[
"X",
"120442599",
"C",
"T"
]
],
[
"207895980042_R15C02",
"locus_0082",
[
"Y",
"15734824",
"C",
"A",
"."
],
"0/1",
[
"Y",
"15734824",
"C",
"A"
]
]
],
"oracle_diploid_candidates_in_haploid_context": [
[
"207895980035_R11C03",
"locus_0125",
[
"X",
"22890860",
"A",
"G,T",
"1"
],
".",
[
"X",
"22890860",
"A",
"G,T"
]
],
[
"207895980035_R11C03",
"locus_0126",
[
"X",
"22890860",
"A",
"G,T",
"1"
],
".",
[
"X",
"22890860",
"A",
"G,T"
]
]
]
},
"unexplained": 0,
"note": "Probe names from the vendor manifest are replaced by stable pseudonyms (locus_NNNN, shared by both oracle files); sample IDs, positions, alleles and all counts are unchanged."
}
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