P5 validated on 2141 1000G samples; control-metric fixes (K-021)

- 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
2026-09-28 10:25:32 +01:00
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commit 80b93e9f45
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+{
+  "n_gtc": 2141,
+  "n_compared": 2141,
+  "errors": [],
+  "byte_identical": 2138,
+  "samples_with_no_field_diff": 2138,
+  "samples_with_field_diff": {
+    "raw_x": 1,
+    "genotypes": 3,
+    "genotype_scores": 3,
+    "base_calls": 3,
+    "call_rate": 2,
+    "logr_dev": 3,
+    "raw_y": 2,
+    "normalization_transforms": 2
+  },
+  "genotype_diff_loci_total": 5,
+  "score_diff_loci_total": 18229,
+  "max_score_abs_diff": 0.9426311254501343,
+  "cluster_files": [
+    "HumanOmni2.5-4v1-Multi_B.egt"
+  ],
+  "sex_agreement_by_version": {
+    "1": 2141,
+    "2": 2129
+  },
+  "ref_sex_counts": {
+    "M": 1054,
+    "F": 1087,
+    "U": 0
+  },
+  "examples": [
+    {
+      "gtc": "/work/omni/data/5767788121/5767788121_R01C01.gtc",
+      "cluster_file": "HumanOmni2.5-4v1-Multi_B.egt",
+      "max_score_abs_diff": 0.6647092700004578,
+      "field_diffs": {
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+        "genotypes": 1,
+        "genotype_scores": 1,
+        "base_calls": 1,
+        "call_rate": [
+          "0.9905122518539429",
+          "0.9905126690864563"
+        ],
+        "logr_dev": [
+          "0.16615425050258636",
+          "0.16615475714206696"
+        ]
+      },
+      "sex_by_version": {
+        "1": "F",
+        "2": "F"
+      },
+      "sex_ref": "F",
+      "byte_identical": false,
+      "ref_layout_canonical": true,
+      "metadata": {
+        "autocall_version": "1.6.2.2",
+        "cluster_file": "HumanOmni2.5-4v1-Multi_B.egt",
+        "imaging_date": "Wednesday, September 07, 2011 11:17:40 PM"
+      }
+    },
+    {
+      "gtc": "/work/omni/data/5826354152/5826354152_R02C01.gtc",
+      "cluster_file": "HumanOmni2.5-4v1-Multi_B.egt",
+      "max_score_abs_diff": 0.9426311254501343,
+      "field_diffs": {
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+        "genotype_scores": 4270,
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+        "normalization_transforms": true,
+        "call_rate": [
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+        ],
+        "logr_dev": [
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+          "0.16252586245536804"
+        ]
+      },
+      "sex_by_version": {
+        "1": "M",
+        "2": "M"
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+      "sex_ref": "M",
+      "byte_identical": false,
+      "ref_layout_canonical": true,
+      "metadata": {
+        "autocall_version": "1.6.2.2",
+        "cluster_file": "HumanOmni2.5-4v1-Multi_B.egt",
+        "imaging_date": "Wednesday, September 07, 2011 10:41:50 PM"
+      }
+    },
+    {
+      "gtc": "/work/omni/data/6268201099/6268201099_R02C01.gtc",
+      "cluster_file": "HumanOmni2.5-4v1-Multi_B.egt",
+      "max_score_abs_diff": 0.37550604343414307,
+      "field_diffs": {
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+        "genotype_scores": 13958,
+        "base_calls": 2,
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+        "logr_dev": [
+          "0.18736381828784943",
+          "0.18737195432186127"
+        ]
+      },
+      "sex_by_version": {
+        "1": "F",
+        "2": "F"
+      },
+      "sex_ref": "F",
+      "byte_identical": false,
+      "ref_layout_canonical": true,
+      "metadata": {
+        "autocall_version": "1.6.2.2",
+        "cluster_file": "HumanOmni2.5-4v1-Multi_B.egt",
+        "imaging_date": "Wednesday, October 19, 2011 1:41:11 AM"
+      }
+    }
+  ],
+  "params": {
+    "preset": "autocall-1.6.2",
+    "norm_version": "1.1.2",
+    "sex_version": 1
+  },
+  "seconds": 1101.9,
+  "passed": false
+}