v2 CN: real-data validation vs NYGC 30x SVs (interim), noise gate on normalised LRR (K-027)

GSE165845 360 arrays: constitutional DEL/DUP calls 77/74 % in the NYGC SV truth, LOH reproduced across replicates 74 %; mosaic calls are mostly false positives (12-23 %), sensitivity for 25 kb-1 Mb events 7-13 % at QUAL >= 20. All samples had been flagged SampleQuality by the summary logr_dev (cluster-file mismatch); the gate now uses the SD of the LRR after the batch reference. Validation script: --ignore-filter. Co-Authored-By: Claude Opus 5.5 <[email protected]> Claude-Session: https://claude.ai/code/session_01814GKVzZVL3FuF3DeiZXhv
2026-09-29 07:42:06 +01:00
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+{
+ "samples": 360,
+ "min_qual": 10.0,
+ "ignored_filters": [
+  "SampleQuality"
+ ],
+ "sensitivity": {
+  "DEL": {
+   "100-500kb": {
+    "found": 230,
+    "truth": 1554,
+    "rate": 0.148
+   },
+   "1000-infkb": {
+    "found": 0,
+    "truth": 15,
+    "rate": 0.0
+   },
+   "25-50kb": {
+    "found": 54,
+    "truth": 225,
+    "rate": 0.24
+   },
+   "50-100kb": {
+    "found": 132,
+    "truth": 894,
+    "rate": 0.1477
+   },
+   "500-1000kb": {
+    "found": 51,
+    "truth": 180,
+    "rate": 0.2833
+   }
+  },
+  "DUP": {
+   "100-500kb": {
+    "found": 279,
+    "truth": 1059,
+    "rate": 0.2635
+   },
+   "1000-infkb": {
+    "found": 9,
+    "truth": 21,
+    "rate": 0.4286
+   },
+   "25-50kb": {
+    "found": 4,
+    "truth": 198,
+    "rate": 0.0202
+   },
+   "50-100kb": {
+    "found": 55,
+    "truth": 462,
+    "rate": 0.119
+   },
+   "500-1000kb": {
+    "found": 19,
+    "truth": 78,
+    "rate": 0.2436
+   }
+  }
+ },
+ "precision": {
+  "DEL": {
+   "in_truth": 473,
+   "calls": 1814,
+   "rate": 0.2607
+  },
+  "DUP": {
+   "in_truth": 367,
+   "calls": 1494,
+   "rate": 0.2456
+  }
+ },
+ "replicate_reproducibility": {
+  "CNV": {
+   "matched": 2132,
+   "comparisons": 6616,
+   "rate": 0.3222
+  },
+  "LOH": {
+   "matched": 400,
+   "comparisons": 532,
+   "rate": 0.7519
+  }
+ },
+ "calls_per_sample_median": 6.0,
+ "loh_calls_per_sample_median": 0.0
+}