{
  "files": {
    "panel": {
      "path": ""
    }
  },
  "rootNode": "MT",
  "nodes": {
    "MT": {
      "label": "MT",
      "type": "BOOL",
      "description": "VariantonMTchrom",
      "query": {
        "field": "#CHROM",
        "operator": "==",
        "value": "chrM"
      },
      "outcomeTrue": {
        "nextNode": "exit_f"
      },
      "outcomeFalse": {
        "nextNode": "blaat"
      },
      "outcomeMissing": {
        "nextNode": "blaat"
      }
    },
    "blaat": {
      "label": "blaat",
      "type": "EXISTS",
      "description": "blaatannotationexists",
      "field": "INFO/CSQ/blaat",
      "outcomeTrue": {
        "nextNode": "csq_exists"
      },
      "outcomeFalse": {
        "nextNode": "csq_exists"
      }
    },
    "csq_exists": {
      "label": "csq_exists",
      "type": "EXISTS",
      "description": "CSQannotationexists",
      "field": "INFO/CSQ/Gene",
      "outcomeTrue": {
        "nextNode": "genepanel"
      },
      "outcomeFalse": {
        "nextNode": "exit_f"
      }
    },
    "genepanel": {
      "label": "genepanel",
      "type": "BOOL",
      "description": "genepanel",
      "query": {
        "field": "INFO/CSQ/Gene",
        "operator": "in",
        "value": "file:panel"
      },
      "outcomeTrue": {
        "nextNode": "mvl"
      },
      "outcomeFalse": {
        "nextNode": "phenotype_match"
      }
    },
    "phenotype_match": {
      "label": "phenotype_match",
      "type": "EXISTS",
      "description": "Phenotypematch",
      "field": "INFO/CSQ/HPO",
      "outcomeTrue": {
        "nextNode": "mvl"
      },
      "outcomeFalse": {
        "nextNode": "exit_f"
      }
    },
    "mvl": {
      "label": "mvl",
      "type": "CATEGORICAL",
      "description": "ManagedVariantListclassification",
      "field": "INFO/VKGL_UMCG",
      "outcomeMap": {
        "P": {
          "nextNode": "exit_t"
        },
        "LP": {
          "nextNode": "exit_t"
        },
        "LB": {
          "nextNode": "exit_f"
        },
        "B": {
          "nextNode": "exit_f"
        }
      },
      "outcomeMissing": {
        "nextNode": "vkgl"
      },
      "outcomeDefault": {
        "nextNode": "vkgl"
      }
    },
    "clinVar": {
      "label": "ClinVar",
      "description": "ClinVar classification",
      "type": "BOOL_MULTI",
      "fields": [
        "INFO/CSQ/clinVar_CLNSIG"
      ],
      "outcomes": [
        {
          "description": "Conflict",
          "queries": [
            {
              "field": "INFO/CSQ/clinVar_CLNSIG",
              "operator": "contains_any",
              "value": [
                "Conflicting_classifications_of_pathogenicity"
              ]
            }
          ],
          "outcomeTrue": {
            "nextNode": "chrom"
          }
        },
        {
          "description": "LP/P",
          "queries": [
            {
              "field": "INFO/CSQ/clinVar_CLNSIG",
              "operator": "contains_any",
              "value": [
                "Likely_pathogenic",
                "Pathogenic"
              ]
            }
          ],
          "outcomeTrue": {
            "nextNode": "exit_lp"
          }
        },
        {
          "description": "VUS",
          "queries": [
            {
              "field": "INFO/CSQ/clinVar_CLNSIG",
              "operator": "contains_any",
              "value": [
                "Uncertain_significance"
              ]
            }
          ],
          "outcomeTrue": {
            "nextNode": "chrom"
          }
        },
        {
          "description": "B/LB",
          "queries": [
            {
              "field": "INFO/CSQ/clinVar_CLNSIG",
              "operator": "contains_any",
              "value": [
                "Likely_benign",
                "Benign"
              ]
            }
          ],
          "outcomeTrue": {
            "nextNode": "exit_lb"
          }
        }
      ],
      "outcomeDefault": {
        "nextNode": "chrom"
      },
      "outcomeMissing": {
        "nextNode": "chrom"
      }
    },
    "vkgl": {
      "label": "vkgl",
      "type": "CATEGORICAL",
      "description": "VKGLclassification",
      "field": "INFO/VKGL",
      "outcomeMap": {
        "P": {
          "nextNode": "exit_t"
        },
        "LP": {
          "nextNode": "exit_t"
        },
        "LB": {
          "nextNode": "exit_f"
        },
        "B": {
          "nextNode": "exit_f"
        }
      },
      "outcomeMissing": {
        "nextNode": "filter"
      },
      "outcomeDefault": {
        "nextNode": "filter"
      }
    },
    "annotSV": {
      "label": "AnnotSV",
      "description": "AnnotSV classification",
      "type": "CATEGORICAL",
      "field": "INFO/CSQ/ASV_ACMG_class",
      "outcomeMap": {
        "5": {
          "nextNode": "exit_p"
        },
        "4": {
          "nextNode": "exit_lp"
        },
        "3": {
          "nextNode": "exit_vus"
        },
        "2": {
          "nextNode": "exit_lb"
        },
        "1": {
          "nextNode": "exit_b"
        }
      },
      "outcomeMissing": {
        "nextNode": "spliceAI"
      },
      "outcomeDefault": {
        "nextNode": "spliceAI"
      }
    },
    "spliceAI": {
      "label": "SpliceAI",
      "description": "SpliceAI prediction",
      "type": "BOOL_MULTI",
      "fields": [
        "INFO/CSQ/SpliceAI_pred_DS_AG",
        "INFO/CSQ/SpliceAI_pred_DS_AL",
        "INFO/CSQ/SpliceAI_pred_DS_DG",
        "INFO/CSQ/SpliceAI_pred_DS_DL"
      ],
      "outcomes": [
        {
          "description": "Delta score (acceptor/donor gain/loss) > 0.42",
          "operator": "OR",
          "queries": [
            {
              "field": "INFO/CSQ/SpliceAI_pred_DS_AG",
              "operator": ">",
              "value": 0.42
            },
            {
              "field": "INFO/CSQ/SpliceAI_pred_DS_AL",
              "operator": ">",
              "value": 0.42
            },
            {
              "field": "INFO/CSQ/SpliceAI_pred_DS_DG",
              "operator": ">",
              "value": 0.42
            },
            {
              "field": "INFO/CSQ/SpliceAI_pred_DS_DL",
              "operator": ">",
              "value": 0.42
            }
          ],
          "outcomeTrue": {
            "nextNode": "exit_lp"
          }
        },
        {
          "description": "Delta score (acceptor/donor gain/loss) > 0.13",
          "operator": "OR",
          "queries": [
            {
              "field": "INFO/CSQ/SpliceAI_pred_DS_AG",
              "operator": ">",
              "value": 0.13
            },
            {
              "field": "INFO/CSQ/SpliceAI_pred_DS_AL",
              "operator": ">",
              "value": 0.13
            },
            {
              "field": "INFO/CSQ/SpliceAI_pred_DS_DG",
              "operator": ">",
              "value": 0.13
            },
            {
              "field": "INFO/CSQ/SpliceAI_pred_DS_DL",
              "operator": ">",
              "value": 0.13
            }
          ],
          "outcomeTrue": {
            "nextNode": "exit_vus"
          }
        }
      ],
      "outcomeDefault": {
        "nextNode": "utr5"
      },
      "outcomeMissing": {
        "nextNode": "utr5"
      }
    },
    "utr5": {
      "label": "5' UTR",
      "description": "5' UTR",
      "type": "EXISTS",
      "field": "INFO/CSQ/five_prime_UTR_variant_consequence",
      "outcomeTrue": {
        "nextNode": "exit_vus"
      },
      "outcomeFalse": {
        "nextNode": "capice"
      }
    },
    "filter": {
      "label": "filter",
      "type": "BOOL",
      "description": "Allfilterspassed",
      "query": {
        "field": "FILTER",
        "operator": "==",
        "value": ["PASS"]
      },
      "outcomeTrue": {
        "nextNode": "artefact"
      },
      "outcomeFalse": {
        "nextNode": "exit_f"
      },
      "outcomeMissing": {
        "nextNode": "artefact"
      }
    },
    "artefact": {
      "label": "artefact",
      "type": "BOOL",
      "description": "Variantonartefactlist",
      "query": {
        "field": "INFO/MVLA",
        "operator": "==",
        "value": "DUMMY"
      },
      "outcomeTrue": {
        "nextNode": "exit_f"
      },
      "outcomeFalse": {
        "nextNode": "exit_f"
      },
      "outcomeMissing": {
        "nextNode": "capice"
      }
    },
    "capice": {
      "label": "capice",
      "type": "BOOL",
      "description": "CAPICEscore>=0.2",
      "query": {
        "field": "INFO/CAP",
        "operator": ">=",
        "value": 0.2
      },
      "outcomeTrue": {
        "nextNode": "gnomad"
      },
      "outcomeFalse": {
        "nextNode": "exit_f"
      },
      "outcomeMissing": {
        "nextNode": "gnomad"
      }
    },
    "gnomad": {
      "label": "gnomad",
      "type": "BOOL",
      "description": "gnomAD_AF<0.02",
      "query": {
        "field": "INFO/CSQ/gnomAD_AF",
        "operator": "<",
        "value": 0.02
      },
      "outcomeTrue": {
        "nextNode": "HLA"
      },
      "outcomeFalse": {
        "nextNode": "exit_f"
      },
      "outcomeMissing": {
        "nextNode": "HLA"
      }
    },
    "HLA": {
      "label": "HLA",
      "type": "BOOL",
      "description": "HLA",
      "query": {
        "field": "INFO/CSQ/SYMBOL",
        "operator": "in",
        "value": ["HLA-A", "HLA-B", "HLA-C", "HLA-DRB1", "HLA-DRB5", "HLA-DQA1", "HLA-DQB1"]
      },
      "outcomeTrue": {
        "nextNode": "exit_f"
      },
      "outcomeFalse": {
        "nextNode": "five_prime"
      },
      "outcomeMissing": {
        "nextNode": "five_prime"
      }
    },
    "five_prime": {
      "label": "five_prime",
      "type": "BOOL",
      "description": "5primeUTR",
      "query": {
        "field": "INFO/CSQ/Consequence",
        "operator": "contains",
        "value": ["5_prime_UTR_variant"]
      },
      "outcomeTrue": {
        "nextNode": "exit_f"
      },
      "outcomeFalse": {
        "nextNode": "inframe"
      },
      "outcomeMissing": {
        "nextNode": "inframe"
      }
    },
    "inframe": {
      "label": "inframe",
      "type": "BOOL",
      "description": "inframeinsertionordeletion",
      "query": {
        "field": "INFO/CSQ/Consequence",
        "operator": "contains_any",
        "value": ["inframe_deletion", "inframe_insertion"]
      },
      "outcomeTrue": {
        "nextNode": "exit_f"
      },
      "outcomeFalse": {
        "nextNode": "splice_acceptor"
      },
      "outcomeMissing": {
        "nextNode": "splice_acceptor"
      }
    },
    "splice_acceptor": {
      "label": "splice_acceptor",
      "type": "BOOL",
      "description": "Spliceacceptor",
      "query": {
        "field": "INFO/CSQ/Consequence",
        "operator": "contains_any",
        "value": ["splice_acceptor_variant", "splice_donor_variant", "splice_region_variant"]
      },
      "outcomeTrue": {
        "nextNode": "exit_t"
      },
      "outcomeFalse": {
        "nextNode": "intron"
      },
      "outcomeMissing": {
        "nextNode": "exit_t"
      }
    },
    "intron": {
      "label": "intron",
      "type": "BOOL",
      "description": "Intron",
      "query": {
        "field": "INFO/CSQ/Consequence",
        "operator": "contains_any",
        "value": ["intron_variant", "synonymous_variant"]
      },
      "outcomeTrue": {
        "nextNode": "exit_f"
      },
      "outcomeFalse": {
        "nextNode": "exit_t"
      },
      "outcomeMissing": {
        "nextNode": "my_multi"
      }
    },
    "my_multi": {
      "label": "my_multi",
      "type": "BOOL_MULTI",
      "fields": ["my_multi_1", "my_multi_2"],
      "outcomeDefault": {
        "nextNode": "exit_t"
      },
      "outcomeMissing": {
        "nextNode": "exit_f"
      },
      "outcomes": [
        {
          "operator": "AND",
          "queries": [
            {
              "field": "my_multi_1",
              "operator": ">",
              "value": 0.1
            },
            {
              "field": "my_multi_1",
              "operator": "<=",
              "value": 0.2
            }
          ],
          "outcomeTrue": {
            "nextNode": "exit_f"
          }
        },
        {
          "operator": "OR",
          "queries": [
            {
              "field": "my_multi_2",
              "operator": "<",
              "value": 0.1
            },
            {
              "field": "my_multi_2",
              "operator": ">",
              "value": 0.2
            }
          ],
          "outcomeTrue": {
            "nextNode": "exit_t"
          }
        }
      ]
    },
    "exit_t": {
      "label": "True",
      "type": "LEAF",
      "class": "T"
    },
    "exit_f": {
      "label": "False",
      "type": "LEAF",
      "class": "F"
    },
    "exit_b": {
      "label": "Benign",
      "type": "LEAF",
      "class": "B"
    },
    "exit_lb": {
      "label": "Likely Benign",
      "type": "LEAF",
      "class": "LB"
    },
    "exit_lt": {
      "label": "Likely T",
      "type": "LEAF",
      "class": "LT"
    },
    "exit_vus": {
      "label": "Unknown Significance",
      "type": "LEAF",
      "class": "VUS"
    },
    "exit_lp": {
      "label": "Likely pathogenic",
      "type": "LEAF",
      "class": "LP"
    },
    "exit_p": {
      "label": "Pathogenic",
      "type": "LEAF",
      "class": "P"
    }
  }
}