sv_config.json

{
  "release_version": "1.0",
  "model_file": "sv_model.joblib",
  "calibrator_file": "sv_calibrator.joblib",
  "calibration": "isotonic regression on out-of-fold scores",
  "features": [
    "is_pass",
    "svtype_DEL",
    "svtype_DUP",
    "svtype_INS",
    "svtype_INV",
    "svtype_BND",
    "svlen_log",
    "cipos_width",
    "ciend_width",
    "is_imprecise",
    "pe_support",
    "sr_support",
    "total_support",
    "vaf",
    "gt_hom",
    "gq",
    "qual_norm",
    "local_depth",
    "gc_min",
    "gc_max",
    "entropy_min",
    "microhom_max",
    "in_segdup_either",
    "in_segdup_both",
    "in_difficult_either",
    "in_difficult_both",
    "in_lowmap_either",
    "in_tandem_either",
    "in_Alu_either",
    "in_L1_either",
    "in_SVA_either",
    "in_LTR_either",
    "frac_span_repeat",
    "n_neighbors",
    "nn_log_dist"
  ],
  "n_features": 35,
  "missing_sentinel": -99999.0,
  "tiers": {
    "HIGH": "CS>=0.70",
    "MODERATE": "0.50<=CS<0.70",
    "WARNING": "0.30<=CS<0.50",
    "LOW": "CS<0.30"
  },
  "tier_edges": [
    0.3,
    0.5,
    0.7
  ],
  "score": "CS = isotonic-calibrated P(call concordant with long-read truth)",
  "variant_class": "SV",
  "sklearn_version_trained": "1.7.1",
  "training": {
    "cohort": "HPRC",
    "n_samples": 208,
    "n_train_rows": 2575116,
    "cv": "5-fold GroupKFold by sample",
    "oof_auroc": 0.9502,
    "oof_auprc": 0.9512
  }
}