CN: final full-cohort cloud validation (GSE165845, CYTO-041/042 defaults)

360 arrays vs NYGC 30x SV: all samples OK (K-027 gate fix), PASS precision DEL 44 % / DUP 57 % (first run 39 % / 34 % with filters ignored), 61 % without the one excess_events array; rare DEL sensitivity 30 %; LOH replicated 85 %. m7g.4xlarge spot, 17 min. docs/validation/V2_cn.md, K-027. Co-Authored-By: Claude Opus 5.5 <[email protected]> Claude-Session: https://claude.ai/code/session_01814GKVzZVL3FuF3DeiZXhv
2026-09-29 23:04:16 +01:00
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+{
+ "samples": 360,
+ "min_qual": 20,
+ "ignored_filters": [],
+ "sensitivity": {
+  "DEL": {
+   "100-500kb": {
+    "found": 128,
+    "truth": 1554,
+    "rate": 0.0824
+   },
+   "1000-infkb": {
+    "found": 0,
+    "truth": 15,
+    "rate": 0.0
+   },
+   "25-50kb": {
+    "found": 12,
+    "truth": 225,
+    "rate": 0.0533
+   },
+   "50-100kb": {
+    "found": 59,
+    "truth": 894,
+    "rate": 0.066
+   },
+   "500-1000kb": {
+    "found": 16,
+    "truth": 180,
+    "rate": 0.0889
+   }
+  },
+  "DUP": {
+   "100-500kb": {
+    "found": 109,
+    "truth": 1059,
+    "rate": 0.1029
+   },
+   "1000-infkb": {
+    "found": 9,
+    "truth": 21,
+    "rate": 0.4286
+   },
+   "25-50kb": {
+    "found": 0,
+    "truth": 198,
+    "rate": 0.0
+   },
+   "50-100kb": {
+    "found": 13,
+    "truth": 462,
+    "rate": 0.0281
+   },
+   "500-1000kb": {
+    "found": 11,
+    "truth": 78,
+    "rate": 0.141
+   }
+  }
+ },
+ "sensitivity_by_carrier_frequency": {
+  "DEL": {
+   "5-20%": {
+    "found": 15,
+    "truth": 285,
+    "rate": 0.0526
+   },
+   "common>=20%": {
+    "found": 1,
+    "truth": 1923,
+    "rate": 0.0005
+   },
+   "rare<5%": {
+    "found": 199,
+    "truth": 660,
+    "rate": 0.3015
+   }
+  },
+  "DUP": {
+   "5-20%": {
+    "found": 21,
+    "truth": 102,
+    "rate": 0.2059
+   },
+   "common>=20%": {
+    "found": 5,
+    "truth": 855,
+    "rate": 0.0058
+   },
+   "rare<5%": {
+    "found": 116,
+    "truth": 861,
+    "rate": 0.1347
+   }
+  }
+ },
+ "precision": {
+  "DEL": {
+   "in_truth": 213,
+   "calls": 480,
+   "rate": 0.4437
+  },
+  "DUP": {
+   "in_truth": 142,
+   "calls": 249,
+   "rate": 0.5703
+  }
+ },
+ "replicate_reproducibility": {
+  "CNV": {
+   "matched": 512,
+   "comparisons": 1458,
+   "rate": 0.3512
+  },
+  "LOH": {
+   "matched": 356,
+   "comparisons": 420,
+   "rate": 0.8476
+  }
+ },
+ "calls_per_sample_median": 1.0,
+ "loh_calls_per_sample_median": 0.0
+}