@molgenis/vip-report-template 7.1.2 → 8.0.0

package/src/mocks/GRCh37/field_metadata.json

@@ -1,794 +0,0 @@
-{
-  "format": {
-    "ADFL": {
-      "label": "Flanking reads",
-      "description": "Number of flanking reads consistent with the allele",
-      "numberType": "NUMBER",
-      "numberCount": 1,
-      "type": "STRING"
-    },
-    "ADIR": {
-      "label": "In-repeat reads",
-      "description": "Number of in-repeat reads consistent with the allele",
-      "numberType": "NUMBER",
-      "numberCount": 1,
-      "type": "STRING"
-    },
-    "ADSP": {
-      "label": "Spanning reads",
-      "description": "Number of spanning reads consistent with the allele",
-      "numberType": "NUMBER",
-      "numberCount": 1,
-      "type": "STRING"
-    },
-    "LC": {
-      "label": "Coverage",
-      "description": "Locus coverage",
-      "numberType": "NUMBER",
-      "numberCount": 1,
-      "type": "FLOAT"
-    },
-    "REPCI": {
-      "label": "Repeat CI",
-      "description": "Confidence interval for the number of repeat units spanned by the allele",
-      "numberType": "NUMBER",
-      "numberCount": 1,
-      "type": "STRING"
-    },
-    "REPCN": {
-      "label": "Repeats",
-      "description": "Number of repeat units spanned by the allele",
-      "numberType": "NUMBER",
-      "numberCount": 1,
-      "type": "STRING"
-    },
-    "VI": {
-      "label": "Inheritance",
-      "description": "An enumeration of possible inheritance modes based on the pedigree of the sample. Potential values: AD, AD_IP, AR, AR_C, XLR, XLD, YL, MT",
-      "numberType": "OTHER",
-      "separator": ",",
-      "type": "CATEGORICAL",
-      "categories": {
-        "AD": {
-          "label": "AD",
-          "description": "Autosomal dominant"
-        },
-        "AD_IP": {
-          "label": "AD_IP",
-          "description": "Autosomal dominant incomplete penetrance"
-        },
-        "AR": {
-          "label": "AR",
-          "description": "Autosomal recessive"
-        },
-        "AR_C": {
-          "label": "AR_C",
-          "description": "Autosomal recessive compound hetrozygote"
-        },
-        "XLD": {
-          "label": "XLD",
-          "description": "X-linked dominant"
-        },
-        "XLR": {
-          "label": "XLR",
-          "description": "X-linked recessive"
-        },
-        "YL": {
-          "label": "YL",
-          "description": "Y-linked"
-        },
-        "MT": {
-          "label": "MT",
-          "description": "Mitochondrial"
-        }
-      }
-    },
-    "VIPC_S": {
-      "label": "VIP sample classification",
-      "numberType": "OTHER",
-      "type": "STRING",
-      "separator": ","
-    }
-  },
-  "info": {
-    "CSQ": {
-      "nestedFields": {
-        "ALLELE_NUM": {
-          "label": "Allele Nr.",
-          "description": "Allele nr within the VCF file.",
-          "numberType": "NUMBER",
-          "numberCount": 1,
-          "type": "INTEGER"
-        },
-        "ALPHSCORE": {
-          "label": "AlphScore",
-          "description": "AlphScore pathogenicity score for missense variants",
-          "numberType": "NUMBER",
-          "numberCount": 1,
-          "type": "FLOAT"
-        },
-        "CAPICE_CL": {
-          "label": "CAPICE",
-          "description": "CAPICE classification",
-          "numberType": "NUMBER",
-          "numberCount": 1,
-          "type": "CATEGORICAL",
-          "categories": {
-            "B": {
-              "label": "B",
-              "description": "Benign"
-            },
-            "LB": {
-              "label": "LB",
-              "description": "Likely benign"
-            },
-            "VUS": {
-              "label": "VUS",
-              "description": "Variant of uncertain significance"
-            },
-            "LP": {
-              "label": "LP",
-              "description": "Likely pathogenic"
-            },
-            "P": {
-              "label": "P",
-              "description": "Pathogenic"
-            }
-          }
-        },
-        "CAPICE_SC": {
-          "label": "CAPICE",
-          "description": "CAPICE pathogenicity score",
-          "numberType": "NUMBER",
-          "numberCount": 1,
-          "type": "FLOAT"
-        },
-        "cDNA_position": {
-          "label": "cDNA pos",
-          "description": "Position within the cDNA.",
-          "numberType": "NUMBER",
-          "numberCount": 1,
-          "type": "STRING"
-        },
-        "CDS_position": {
-          "label": "CDS pos",
-          "description": "Position within the coding sequence.",
-          "numberType": "NUMBER",
-          "numberCount": 1,
-          "type": "STRING"
-        },
-        "CLIN_SIG": {
-          "label": "ClinVar",
-          "description": "ClinVar classification(s)",
-          "numberType": "OTHER",
-          "separator": "&",
-          "type": "STRING"
-        },
-        "clinVar": {
-          "label": "ClinVar ID",
-          "description": "ClinVar Variation ID",
-          "numberType": "OTHER",
-          "type": "INTEGER"
-        },
-        "clinVar_CLNID": {
-          "label": "ClinVar ID",
-          "description": "ClinVar Variation ID",
-          "numberType": "OTHER",
-          "type": "INTEGER"
-        },
-        "clinVar_CLNSIG": {
-          "label": "ClinVar",
-          "description": "Clinical significance for this single variant",
-          "numberType": "OTHER",
-          "separator": "&",
-          "type": "CATEGORICAL",
-          "categories": {
-            "Benign": {
-              "label": "B",
-              "description": "Benign"
-            },
-            "Likely_benign": {
-              "label": "LB",
-              "description": "Likely benign"
-            },
-            "Uncertain_significance": {
-              "label": "VUS",
-              "description": "Variant of uncertain significance"
-            },
-            "Likely_pathogenic": {
-              "label": "LP",
-              "description": "Likely pathogenic"
-            },
-            "Pathogenic": {
-              "label": "P",
-              "description": "Pathogenic"
-            },
-            "Conflicting_interpretations_of_pathogenicity": {
-              "label": "Conflict",
-              "description": "Conflicting interpretations of pathogenicity"
-            }
-          }
-        },
-        "clinVar_CLNSIGINCL": {
-          "label": "ClinVar variant combination",
-          "description": "Clinical significance for a haplotype or genotype that includes this variant",
-          "numberType": "OTHER",
-          "separator": "&",
-          "type": "CATEGORICAL",
-          "categories": {
-            "Benign": {
-              "label": "B",
-              "description": "Benign"
-            },
-            "Likely_benign": {
-              "label": "LB",
-              "description": "Likely benign"
-            },
-            "Uncertain_significance": {
-              "label": "VUS",
-              "description": "Variant of uncertain significance"
-            },
-            "Likely_pathogenic": {
-              "label": "LP",
-              "description": "Likely pathogenic"
-            },
-            "Pathogenic": {
-              "label": "P",
-              "description": "Pathogenic"
-            },
-            "Conflicting_interpretations_of_pathogenicity": {
-              "label": "Conflict",
-              "description": "Conflicting interpretations of pathogenicity"
-            }
-          }
-        },
-        "clinVar_CLNREVSTAT": {
-          "label": "ClinVar status",
-          "description": "ClinVar review status",
-          "numberType": "OTHER",
-          "separator": "&",
-          "type": "CATEGORICAL",
-          "categories": {
-            "practice_guideline": {
-              "label": "Practice guideline",
-              "description": "There is a submitted record with a classification from a practice guideline"
-            },
-            "reviewed_by_expert_panel": {
-              "label": "Reviewed by expert panel",
-              "description": "There is a submitted record with a classification from an expert panel"
-            },
-            "criteria_provided": {
-              "label": "Criteria provided",
-              "description": "Assertion criteria and evidence for the classification (or a public contact) were provided"
-            },
-            "_multiple_submitters": {
-              "label": "Multiple submitters",
-              "description": "There are multiple submitted records with a classification"
-            },
-            "_no_conflicts": {
-              "label": "No conflicts",
-              "description": "The classifications agree"
-            },
-            "_single_submitter": {
-              "label": "Single submitter",
-              "description": "There is a single submitted record with a classification"
-            },
-            "_conflicting_interpretations": {
-              "label": "Conflicting_interpretations",
-              "description": "There are conflicting classifications"
-            },
-            "no_assertion_criteria_provided": {
-              "label": "No assertion criteria provided",
-              "description": "There are one or more submitted records with a classification but without assertion criteria and evidence for the classification (or a public contact)"
-            },
-            "no_assertion_provided": {
-              "label": "No assertion provided"
-            }
-          }
-        },
-        "Consequence": {
-          "label": "Effect",
-          "description": "Effect(s) described as Sequence Ontology term(s)",
-          "numberType": "OTHER",
-          "separator": "&",
-          "type": "STRING"
-        },
-        "Existing_variation": {
-          "label": "Ex. var.",
-          "description": "Existing variation.",
-          "numberType": "OTHER",
-          "separator": "&",
-          "type": "STRING"
-        },
-        "FATHMM_MKL_NC": {
-          "label": "FATHMM-MKL-NC",
-          "description": "Predict the Functional Consequences of Non-Coding Single Nucleotide Variants (SNVs)",
-          "numberType": "NUMBER",
-          "numberCount": 1,
-          "type": "FLOAT"
-        },
-        "GDB_PRO": {
-          "label": "GDB_PRO",
-          "description": "Highest GREEN-DB constraint score for overlapping promotor regions.",
-          "numberType": "NUMBER",
-          "numberCount": 1,
-          "type": "FLOAT"
-        },
-        "GDB_ENH": {
-          "label": "GDB_ENH",
-          "description": "Highest GREEN-DB constraint score for overlapping enhancer regions.",
-          "numberType": "NUMBER",
-          "numberCount": 1,
-          "type": "FLOAT"
-        },
-        "GDB_BIV": {
-          "label": "GDB_BIV",
-          "description": "Highest GREEN-DB constraint score for overlapping bivalent regions.",
-          "numberType": "NUMBER",
-          "numberCount": 1,
-          "type": "FLOAT"
-        },
-        "GDB_SIL": {
-          "label": "GDB_SIL",
-          "description": "Highest GREEN-DB constraint score for overlapping silencer regions.",
-          "numberType": "NUMBER",
-          "numberCount": 1,
-          "type": "FLOAT"
-        },
-        "GDB_INS": {
-          "label": "GDB_INS",
-          "description": "Highest GREEN-DB constraint score for overlapping insulater regions.",
-          "numberType": "NUMBER",
-          "numberCount": 1,
-          "type": "FLOAT"
-        },
-        "Feature_type": {
-          "label": "Feature Type.",
-          "description": "The VEP feature type",
-          "numberType": "NUMBER",
-          "numberCount": 1,
-          "type": "CATEGORICAL",
-          "categories": {
-            "Transcript": {
-              "label": "Transcript",
-              "description": "Transcript"
-            },
-            "RegulatoryFeature": {
-              "label": "Regulatory",
-              "description": "Regulatory feature"
-            },
-            "MotifFeature": {
-              "label": "Motif",
-              "description": "Motif feature"
-            }
-          },
-          "required": true
-        },
-        "FLAGS": {
-          "label": "Flags",
-          "description": "Flags",
-          "numberType": "OTHER",
-          "separator": "&",
-          "type": "STRING"
-        },
-        "GADO_PD": {
-          "label": "GADO_PD",
-          "description": "Gene-phenotypes association based on the GeneNetwork Assisted Diagnostic Optimization (GADO) gene prioritization Z-scores, see https://www.genenetwork.nl/gado and https://doi.org/10.1038/s41467-019-10649-4",
-          "numberType": "NUMBER",
-          "numberCount": 1,
-          "type": "CATEGORICAL",
-          "categories": {
-            "HC": {
-              "label": "High confidence",
-              "description": "Z-Score >= 5"
-            },
-            "LC": {
-              "label": "Low confidence",
-              "description": "Z-Score >= 3 and < 5"
-            }
-          }
-        },
-        "GADO_SC": {
-          "label": "GADO_SC",
-          "description": "The combined prioritization GADO Z-score over the HPO of the proband(s) terms for this case.",
-          "numberType": "NUMBER",
-          "numberCount": 1,
-          "type": "FLOAT"
-        },
-        "gnomAD_AF": {
-          "label": "gnomAD AF",
-          "description": "gnomAD allele frequency",
-          "numberType": "NUMBER",
-          "numberCount": 1,
-          "type": "FLOAT"
-        },
-        "gnomAD_COV": {
-          "label": "gnomAD COV",
-          "description": "gnomAD coverage (percent of individuals in gnomAD source)",
-          "numberType": "NUMBER",
-          "numberCount": 1,
-          "type": "FLOAT"
-        },
-        "gnomAD_FAF95": {
-          "label": "gnomAD FAF95",
-          "description": "gnomAD filter allele frequency (95% confidence)",
-          "numberType": "NUMBER",
-          "numberCount": 1,
-          "type": "FLOAT"
-        },
-        "gnomAD_FAF99": {
-          "label": "gnomAD FAF99",
-          "description": "gnomAD filter allele frequency (99% confidence)",
-          "numberType": "NUMBER",
-          "numberCount": 1,
-          "type": "FLOAT"
-        },
-        "gnomAD_HN": {
-          "label": "gnomAD HN",
-          "description": "gnomAD number of homozygotes",
-          "numberType": "NUMBER",
-          "numberCount": 1,
-          "type": "INTEGER"
-        },
-        "gnomAD_SRC": {
-          "label": "gnomAD SRC",
-          "description": "gnomAD source",
-          "numberType": "NUMBER",
-          "numberCount": 1,
-          "type": "CATEGORICAL",
-          "categories": {
-            "E": {
-              "label": "Exomes"
-            },
-            "G": {
-              "label": "Genomes"
-            },
-            "T": {
-              "label": "Total",
-              "description": "Total: exomes & genomes"
-            }
-          }
-        },
-        "gnomAD_QC": {
-          "label": "gnomAD QC",
-          "description": "gnomAD quality control filters that failed",
-          "numberType": "OTHER",
-          "separator": "&",
-          "type": "STRING"
-        },
-        "HGNC_ID": {
-          "label": "HGNC ID",
-          "description": "The HGNC gene ID",
-          "numberType": "NUMBER",
-          "numberCount": 1,
-          "type": "INTEGER"
-        },
-        "HGVSc": {
-          "label": "HGVS C",
-          "description": "HGVS nomenclature: coding DNA reference sequence",
-          "numberType": "NUMBER",
-          "numberCount": 1,
-          "type": "STRING"
-        },
-        "HGVSp": {
-          "label": "HGVS P",
-          "description": "HGVS nomenclature: protein reference sequence",
-          "numberType": "NUMBER",
-          "numberCount": 1,
-          "type": "STRING"
-        },
-        "HPO": {
-          "label": "HPO",
-          "description": "Human Phenotype Ontology (HPO) terms describing phenotypic abnormalities, see https://hpo.jax.org/ and https://doi.org/10.1093/nar/gkad1005",
-          "numberType": "OTHER",
-          "separator": "&",
-          "type": "STRING"
-        },
-        "IMPACT": {
-          "label": "Impact",
-          "description": "The Impact as predicted by VEP",
-          "numberType": "NUMBER",
-          "numberCount": 1,
-          "type": "CATEGORICAL",
-          "categories": {
-            "LOW": {
-              "label": "Low"
-            },
-            "MODERATE": {
-              "label": "Moderate"
-            },
-            "HIGH": {
-              "label": "High"
-            },
-            "MODIFIER": {
-              "label": "Modifier"
-            }
-          },
-          "required": true
-        },
-        "IncompletePenetrance": {
-          "label": "Gene: Inc.Pen.",
-          "description": "Is gene associated with incomplete penetrance?",
-          "numberType": "NUMBER",
-          "numberCount": 1,
-          "type": "CATEGORICAL",
-          "categories": {
-            "1": {
-              "label": "True",
-              "description": "Gene is associated with incomplete penetrance"
-            }
-          },
-          "nullValue": {
-            "label": "False"
-          }
-        },
-        "InheritanceModesGene": {
-          "label": "Inh.Pat.",
-          "description": "Inheritance pattern",
-          "numberType": "OTHER",
-          "separator": "&",
-          "type": "CATEGORICAL",
-          "categories": {
-            "AD": {
-              "label": "AD",
-              "description": "Autosomal dominant"
-            },
-            "AD_IP": {
-              "label": "AD_IP",
-              "description": "Autosomal dominant incomplete penetrance"
-            },
-            "AR": {
-              "label": "AR",
-              "description": "Autosomal recessive"
-            },
-            "AR_C": {
-              "label": "AR_C",
-              "description": "Autosomal recessive compound hetrozygote"
-            },
-            "XL": {
-              "label": "XL",
-              "description": "X-linked"
-            },
-            "XLD": {
-              "label": "XLD",
-              "description": "X-linked dominant"
-            },
-            "XLR": {
-              "label": "XLR",
-              "description": "X-linked recessive"
-            },
-            "YL": {
-              "label": "YL",
-              "description": "Y-linked"
-            },
-            "MT": {
-              "label": "MT",
-              "description": "Mitochondrial"
-            }
-          }
-        },
-        "ncER": {
-          "label": "ncER",
-          "description": "Non-coding essential regulation, from: 0(probably not essential for regulation) to 100 (probably essential for regulation).",
-          "numberType": "NUMBER",
-          "numberCount": 1,
-          "type": "FLOAT"
-        },
-        "PHENO": {
-          "label": "Pheno",
-          "description": "Phenotype match.",
-          "numberType": "OTHER",
-          "separator": "&",
-          "type": "INTEGER"
-        },
-        "PICK": {
-          "label": "PICK",
-          "description": "Boolean indicating if this is the VEP picked transcript.",
-          "numberType": "NUMBER",
-          "numberCount": 1,
-          "type": "INTEGER"
-        },
-        "PolyPhen": {
-          "label": "PolyPhen",
-          "description": "PolyPhen score.",
-          "numberType": "NUMBER",
-          "numberCount": 1,
-          "type": "FLOAT"
-        },
-        "Protein_position": {
-          "label": "Protein pos",
-          "description": "Position within the protein.",
-          "numberType": "NUMBER",
-          "numberCount": 1,
-          "type": "STRING"
-        },
-        "PUBMED": {
-          "label": "PubMed",
-          "description": "PubMed citations",
-          "numberType": "OTHER",
-          "separator": "&",
-          "type": "INTEGER"
-        },
-        "ReMM": {
-          "label": "ReMM",
-          "description": "The Regulatory Mendelian Mutation (ReMM) score was created for relevance prediction of non-coding variations (SNVs and small InDels) in the human genome (hg19) in terms of Mendelian diseases.",
-          "numberType": "NUMBER",
-          "numberCount": 1,
-          "type": "FLOAT"
-        },
-        "SIFT": {
-          "label": "SIFT",
-          "description": "SIFT score.",
-          "numberType": "NUMBER",
-          "numberCount": 1,
-          "type": "FLOAT"
-        },
-        "SOMATIC": {
-          "label": "Somatic",
-          "description": "Somatic.",
-          "numberType": "OTHER",
-          "separator": "&",
-          "type": "INTEGER"
-        },
-        "SpliceAI_pred_DS_AG": {
-          "label": "SpliceAI AG",
-          "description": "SpliceAI Delta score (acceptor gain).",
-          "numberType": "NUMBER",
-          "numberCount": 1,
-          "type": "FLOAT"
-        },
-        "SpliceAI_pred_DS_AL": {
-          "label": "SpliceAI AL",
-          "description": "SpliceAI Delta score (acceptor loss).",
-          "numberType": "NUMBER",
-          "numberCount": 1,
-          "type": "FLOAT"
-        },
-        "SpliceAI_pred_DS_DG": {
-          "label": "SpliceAI DG",
-          "description": "SpliceAI Delta score (donor gain).",
-          "numberType": "NUMBER",
-          "numberCount": 1,
-          "type": "FLOAT"
-        },
-        "SpliceAI_pred_DS_DL": {
-          "label": "SpliceAI DL",
-          "description": "SpliceAI Delta score (donor loss).",
-          "numberType": "NUMBER",
-          "numberCount": 1,
-          "type": "FLOAT"
-        },
-        "STRAND": {
-          "label": "Strand",
-          "description": "The strand of the gene (0=- 1=+).",
-          "numberType": "NUMBER",
-          "numberCount": 1,
-          "type": "INTEGER"
-        },
-        "SYMBOL": {
-          "label": "Gene",
-          "description": "Gene symbol",
-          "numberType": "NUMBER",
-          "numberCount": 1,
-          "type": "STRING"
-        },
-        "VIPC": {
-          "label": "VIP classification",
-          "description": "Variant consequence classification predicted by the Variant Interpretation Pipeline (VIP), see https://vip.molgeniscloud.org/ and https://doi.org/10.1101/2024.04.11.24305656",
-          "numberType": "NUMBER",
-          "numberCount": 1,
-          "type": "STRING",
-          "required": true
-        },
-        "VIPP": {
-          "label": "VIP path",
-          "description": "VIP decision tree path",
-          "numberType": "OTHER",
-          "separator": "&",
-          "type": "STRING",
-          "required": true
-        },
-        "VKGL_CL": {
-          "label": "VKGL",
-          "description": "Variant consensus classification from the Vereniging Klinisch Genetische Laboratoriumdiagnostiek (VKGL) datashare database, see https://vkgl.nl/nl/diagnostiek/vkgl-datashare-database",
-          "numberType": "NUMBER",
-          "numberCount": 1,
-          "type": "CATEGORICAL",
-          "categories": {
-            "B": {
-              "label": "B",
-              "description": "Benign"
-            },
-            "LB": {
-              "label": "LB",
-              "description": "Likely benign"
-            },
-            "VUS": {
-              "label": "VUS",
-              "description": "Variant of uncertain significance"
-            },
-            "LP": {
-              "label": "LP",
-              "description": "Likely pathogenic"
-            },
-            "P": {
-              "label": "P",
-              "description": "Pathogenic"
-            }
-          }
-        },
-        "VKGL_UMCG": {
-          "label": "MVL",
-          "description": "UMCG managed variant list classification",
-          "numberType": "NUMBER",
-          "numberCount": 1,
-          "type": "CATEGORICAL",
-          "categories": {
-            "B": {
-              "label": "B",
-              "description": "Benign"
-            },
-            "LB": {
-              "label": "LB",
-              "description": "Likely benign"
-            },
-            "VUS": {
-              "label": "VUS",
-              "description": "Variant of uncertain significance"
-            },
-            "LP": {
-              "label": "LP",
-              "description": "Likely pathogenic"
-            },
-            "P": {
-              "label": "P",
-              "description": "Pathogenic"
-            }
-          }
-        }
-      }
-    },
-    "STR_NORMAL_MAX": {
-      "label": "STR normal max",
-      "description": "Maximum number of repeats allowed to call as normal as defined in the Stranger catalogue",
-      "numberType": "NUMBER",
-      "numberCount": 1,
-      "type": "INTEGER"
-    },
-    "STR_PATHOLOGIC_MIN": {
-      "label": "STR pathologic min",
-      "description": "Mininum number of repeats required to call as pathologic as defined in the Stranger catalogue",
-      "numberType": "NUMBER",
-      "numberCount": 1,
-      "type": "INTEGER"
-    },
-    "STR_STATUS": {
-      "label": "STR status",
-      "description": "Repeat expansion status as decided by Stranger",
-      "numberType": "PER_ALT",
-      "separator": ",",
-      "type": "CATEGORICAL",
-      "categories": {
-        "normal": {
-          "label": "normal",
-          "description": "Repeat count is smaller than or equal to the maximum number of repeats allowed to call as normal"
-        },
-        "pre_mutation": {
-          "label": "pre-mutation",
-          "description": "Repeat count is greater than the maximum number of repeats allowed to call as normal and smaller than the minimum number of repeats required to call as pathologic"
-        },
-        "full_mutation": {
-          "label": "full-mutation",
-          "description": "Repeat count is greater than or equal to the minimum number of repeats required to call as pathologic"
-        }
-      }
-    },
-    "SVTYPE": {
-      "label": "SV type",
-      "description": "Type of structural variant",
-      "numberType": "NUMBER",
-      "numberCount": 1,
-      "type": "STRING"
-    }
-  }
-}