{
  "rootNode": "type",
  "nodes": {
    "type": {
      "label": "STR?",
      "description": "Is STR?",
      "type": "BOOL",
      "query": {
        "field": "INFO/SVTYPE",
        "operator": "==",
        "value": "STR"
      },
      "outcomeTrue": {
        "nextNode": "pick"
      },
      "outcomeFalse": {
        "nextNode": "filter"
      },
      "outcomeMissing": {
        "nextNode": "filter"
      }
    },
    "pick": {
      "label": "Picked Transcript?",
      "description": "is picked transcript",
      "type": "BOOL",
      "query": {
        "field": "INFO/CSQ/PICK",
        "operator": "==",
        "value": 1
      },
      "outcomeTrue": {
        "nextNode": "gene_str"
      },
      "outcomeFalse": {
        "nextNode": "exit_rm"
      },
      "outcomeMissing": {
        "nextNode": "exit_rm"
      }
    },
    "gene_str": {
      "label": "Gene",
      "description": "Gene exists",
      "type": "EXISTS",
      "field": "INFO/CSQ/Gene",
      "outcomeTrue": {
        "nextNode": "up_downstream"
      },
      "outcomeFalse": {
        "nextNode": "exit_rm"
      }
    },
    "up_downstream": {
      "label": "Up or downstream",
      "description": "Up or downstream gene variant",
      "type": "BOOL",
      "query": {
        "field": "INFO/CSQ/Consequence",
        "operator": "contains_any",
        "value": ["upstream_gene_variant", "downstream_gene_variant"]
      },
      "outcomeTrue": {
        "nextNode": "exit_rm"
      },
      "outcomeFalse": {
        "nextNode": "unit"
      },
      "outcomeMissing": {
        "nextNode": "unit"
      }
    },
    "unit": {
      "label": "STR Unit",
      "description": "Called unit equals configured unit",
      "type": "BOOL",
      "query": {
        "field": "INFO/RUMATCH",
        "operator": "==",
        "value": true
      },
      "outcomeTrue": {
        "nextNode": "status"
      },
      "outcomeFalse": {
        "nextNode": "exit_vus"
      },
      "outcomeMissing": {
        "nextNode": "exit_vus"
      }
    },
    "status": {
      "label": "Status",
      "description": "STR mutation status",
      "type": "CATEGORICAL",
      "field": "INFO/STR_STATUS",
      "outcomeMap": {
        "pre_mutation": {
          "nextNode": "exit_vus"
        },
        "normal": {
          "nextNode": "exit_lb"
        },
        "full_mutation": {
          "nextNode": "exit_lp"
        }
      },
      "outcomeMissing": {
        "nextNode": "exit_vus"
      },
      "outcomeDefault": {
        "nextNode": "exit_vus"
      }
    },
    "filter": {
      "label": "Filter",
      "description": "Filter pass",
      "type": "BOOL",
      "query": {
        "field": "FILTER",
        "operator": "==",
        "value": ["PASS"]
      },
      "outcomeTrue": {
        "nextNode": "vkgl"
      },
      "outcomeFalse": {
        "nextNode": "exit_lq"
      },
      "outcomeMissing": {
        "nextNode": "vkgl"
      }
    },
    "vkgl": {
      "label": "VKGL",
      "description": "VKGL classification",
      "type": "CATEGORICAL",
      "field": "INFO/CSQ/VKGL_CL",
      "outcomeMap": {
        "P": {
          "nextNode": "exit_p"
        },
        "LP": {
          "nextNode": "exit_lp"
        },
        "VUS": {
          "nextNode": "clinVar"
        },
        "LB": {
          "nextNode": "exit_lb"
        },
        "B": {
          "nextNode": "exit_b"
        }
      },
      "outcomeMissing": {
        "nextNode": "clinVar"
      },
      "outcomeDefault": {
        "nextNode": "clinVar"
      }
    },
    "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_interpretations_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"
      }
    },
    "chrom": {
      "label": "Chromosome",
      "description": "Chromosome 1-22-X-Y-MT",
      "type": "BOOL",
      "query": {
        "field": "#CHROM",
        "operator": "in",
        "value": [
          "chr1",
          "chr2",
          "chr3",
          "chr4",
          "chr5",
          "chr6",
          "chr7",
          "chr8",
          "chr9",
          "chr10",
          "chr11",
          "chr12",
          "chr13",
          "chr14",
          "chr15",
          "chr16",
          "chr17",
          "chr18",
          "chr19",
          "chr20",
          "chr21",
          "chr22",
          "chrX",
          "chrY",
          "chrM"
        ]
      },
      "outcomeTrue": {
        "nextNode": "gene"
      },
      "outcomeFalse": {
        "nextNode": "exit_rm"
      },
      "outcomeMissing": {
        "nextNode": "gene"
      }
    },
    "gene": {
      "label": "Gene",
      "description": "Gene exists",
      "type": "EXISTS",
      "field": "INFO/CSQ/Gene",
      "outcomeTrue": {
        "nextNode": "gnomAD"
      },
      "outcomeFalse": {
        "nextNode": "exit_rm"
      }
    },
    "sv": {
      "label": "SV?",
      "description": "Structural Variant?",
      "type": "EXISTS",
      "field": "INFO/SVTYPE",
      "outcomeTrue": {
        "nextNode": "str"
      },
      "outcomeFalse": {
        "nextNode": "spliceAI"
      }
    },
    "str": {
      "label": "STR?",
      "description": "Short tandem repeat?",
      "type": "BOOL",
      "query": {
        "field": "INFO/SVTYPE",
        "operator": "==",
        "value": "STR"
      },
      "outcomeTrue": {
        "nextNode": "str_status"
      },
      "outcomeFalse": {
        "nextNode": "annotSV"
      },
      "outcomeMissing": {
        "nextNode": "annotSV"
      }
    },
    "str_status": {
      "label": "STR status",
      "description": "Stranger str status (normal, pre_mutation, mutation)",
      "type": "CATEGORICAL",
      "field": "INFO/STR_STATUS",
      "outcomeMap": {
        "full_mutation": {
          "nextNode": "exit_lp"
        },
        "pre_mutation": {
          "nextNode": "exit_vus"
        },
        "normal": {
          "nextNode": "exit_lb"
        }
      },
      "outcomeMissing": {
        "nextNode": "exit_vus"
      },
      "outcomeDefault": {
        "nextNode": "exit_vus"
      }
    },
    "gnomAD": {
      "label": "GnomAD",
      "description": "gnomAD QC filter failure",
      "type": "EXISTS",
      "field": "INFO/CSQ/gnomAD_QC",
      "outcomeTrue": {
        "nextNode": "sv"
      },
      "outcomeFalse": {
        "nextNode": "gnomAD_AF"
      }
    },
    "gnomAD_AF": {
      "label": "",
      "description": "gnomAD",
      "type": "BOOL_MULTI",
      "fields": ["INFO/CSQ/gnomAD_FAF99", "INFO/CSQ/gnomAD_HN"],
      "outcomes": [
        {
          "description": "Filtering allele Frequency (99% confidence) >= 0.02 or Number of Homozygotes > 5",
          "operator": "OR",
          "queries": [
            {
              "field": "INFO/CSQ/gnomAD_FAF99",
              "operator": ">=",
              "value": 0.02
            },
            {
              "field": "INFO/CSQ/gnomAD_HN",
              "operator": ">=",
              "value": 5
            }
          ],
          "outcomeTrue": {
            "nextNode": "exit_lb"
          }
        }
      ],
      "outcomeDefault": {
        "nextNode": "sv"
      },
      "outcomeMissing": {
        "nextNode": "sv"
      }
    },
    "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"
      }
    },
    "capice": {
      "label": "Capice",
      "description": "CAPICE prediction > 0.5",
      "type": "BOOL",
      "query": {
        "field": "INFO/CSQ/CAPICE_SC",
        "operator": ">",
        "value": 0.5
      },
      "outcomeTrue": {
        "nextNode": "exit_lp"
      },
      "outcomeFalse": {
        "nextNode": "exit_lb"
      },
      "outcomeMissing": {
        "nextNode": "exit_vus"
      }
    },
    "exit_lq": {
      "label": "Low Quality",
      "description": "Low Quality",
      "type": "LEAF",
      "class": "LQ"
    },
    "exit_rm": {
      "label": "",
      "description": "Remove",
      "type": "LEAF",
      "class": "RM"
    },
    "exit_b": {
      "label": "Benign",
      "description": "Benign",
      "type": "LEAF",
      "class": "B"
    },
    "exit_lb": {
      "label": "Likely Benign",
      "description": "Likely Benign",
      "type": "LEAF",
      "class": "LB"
    },
    "exit_vus": {
      "label": "Uncertain Significance",
      "description": "Uncertain Significance",
      "type": "LEAF",
      "class": "VUS"
    },
    "exit_lp": {
      "label": "Likely Pathogenic",
      "description": "Likely Pathogenic",
      "type": "LEAF",
      "class": "LP"
    },
    "exit_p": {
      "label": "Pathogenic",
      "description": "Pathogenic",
      "type": "LEAF",
      "class": "P"
    }
  }
}