@molgenis/vip-report-template 8.3.2 → 8.4.0

package/package.json

@@ -1,34 +1,34 @@
 {
   "name": "@molgenis/vip-report-template",
-  "version": "8.3.2",
+  "version": "8.4.0",
   "description": "Report Template for Variant Call Format (VCF) Report Generator",
   "license": "LGPL-3.0",
   "devDependencies": {
-    "@molgenis/vite-plugin-inline": "^2.0.1",
+    "@molgenis/vite-plugin-inline": "^2.0.2",
     "@types/async-lock": "^1.4.2",
-    "@types/node": "^24.12.0",
-    "@vitest/coverage-v8": "^4.1.2",
+    "@types/node": "^24.12.2",
+    "@vitest/coverage-v8": "^4.1.3",
     "async-lock": "^1.4.1",
     "bulma": "^1.0.4",
-    "esbuild": "^0.27.4",
-    "eslint": "^10.1.0",
+    "esbuild": "^0.28.0",
+    "eslint": "^10.2.0",
     "eslint-config-prettier": "^10.1.8",
     "eslint-plugin-solid": "^0.14.5",
     "husky": "^9.1.7",
-    "jsdom": "^29.0.1",
+    "jsdom": "^29.0.2",
     "prettier": "^3.8.1",
-    "sass": "^1.98.0",
+    "sass": "^1.99.0",
     "typescript": "^6.0.2",
     "typescript-eslint": "^8.58.0",
-    "vite": "^8.0.3",
-    "vite-plugin-solid": "^2.11.11",
-    "vitest": "^4.1.2"
+    "vite": "^8.0.7",
+    "vite-plugin-solid": "^2.11.12",
+    "vitest": "^4.1.3"
   },
   "dependencies": {
     "@fortawesome/fontawesome-svg-core": "^7.2.0",
     "@fortawesome/free-solid-svg-icons": "^7.2.0",
-    "@molgenis/vip-report-api": "7.0.6",
-    "@molgenis/vip-report-vcf": "^4.0.7",
+    "@molgenis/vip-report-api": "7.0.7",
+    "@molgenis/vip-report-vcf": "^4.0.8",
     "@solidjs/router": "^0.16.1",
     "ajv": "^8.18.0",
     "base64-js": "^1.5.1",

package/src/assets/sass/main.scss

@@ -93,4 +93,12 @@ table.is-borderless td,
   white-space: nowrap;
   overflow: hidden;
   text-overflow: ellipsis;
+}
+
+.small-blue-link {
+  display: inline;
+  font-size: 0.8rem;
+  color: #1d4ed8;
+  text-decoration: none;
+  font-weight: normal;
 }

package/src/components/VariantConsequenceContainer.tsx

@@ -1,4 +1,4 @@
-import { Component, Show } from "solid-js";
+import { Component, createSignal, Show } from "solid-js";
 import { MetadataContainer, SampleContainer } from "../utils/api.ts";
 import { VcfRecord } from "@molgenis/vip-report-vcf";
 import { DecisionTree, Item, Sample } from "@molgenis/vip-report-api";
@@ -12,6 +12,7 @@ import { getPedigreeSamples } from "../utils/sample.ts";
 import { ConfigJson } from "../types/config";
 import { VariantGenotypeTable } from "./VariantGenotypeTable.tsx";
 import { initConfig } from "../utils/config/config.ts";
+import { A } from "@solidjs/router";
 
 export const VariantConsequenceContainer: Component<{
   config: ConfigJson;
@@ -36,66 +37,84 @@ export const VariantConsequenceContainer: Component<{
     }
     return false;
   };
+  const [showEmptyInfo, setShowEmptyInfo] = createSignal(false);
+  const toggleShowEmptyInfo = () => setShowEmptyInfo((isShow) => !isShow);
+  const [showEmptyCsq, setShowEmptyCsq] = createSignal(false);
+  const toggleShowEmptyCsq = () => setShowEmptyCsq((isShow) => !isShow);
 
   return (
-    <>
-      <div class="columns">
-        <div class="column is-4">
-          <div>
-            <h1 class="title is-5">Info</h1>
-            <VariantInfoTable variantType={props.variantType} metadata={props.metadata} record={props.record} />
-          </div>
-          <div class="mt-3">
-            <h1 class="title is-5">Consequence</h1>
-            <VariantConsequenceTable
-              variantType={props.variantType}
-              metadata={props.metadata}
-              record={props.record}
-              consequenceId={props.consequenceId}
-            />
-          </div>
-          <div class="mt-3">
-            <h1 class="title is-5">Record</h1>
-            <VariantTable variant={props.record.data} />
-          </div>
+    <div class="columns">
+      <div class="column is-4">
+        <div>
+          <h1 class="title is-5">
+            Info
+            <A href="#" onClick={toggleShowEmptyInfo} class="small-blue-link">
+              {showEmptyInfo() ? "(Hide empty fields)" : "(Show empty fields)"}
+            </A>
+          </h1>
+          <VariantInfoTable
+            variantType={props.variantType}
+            metadata={props.metadata}
+            record={props.record}
+            isShowEmpty={showEmptyInfo()}
+          />
         </div>
-        <div class="column is-8">
-          <Show when={config().variant.samplesCells}>
-            {(samplesCells) => (
-              <div class="column">
-                <h1 class="title is-5">Samples</h1>
-                <VariantGenotypeTable
-                  config={samplesCells()}
-                  samples={samples()}
-                  metadata={props.metadata}
-                  variantType={props.variantType}
-                  record={props.record}
-                />
-              </div>
-            )}
-          </Show>
-          <div class="columns mt-3">
-            {props.decisionTree !== null && hasDecisionTreePathMeta() && (
-              <div class="column is-6">
-                <h1 class="title is-5">Variant classification tree path</h1>
-                <DecisionTreePath
-                  decisionTree={props.decisionTree}
-                  path={getDecisionTreePath(props.metadata.records, props.record, props.consequenceId)}
-                />
-              </div>
-            )}
-            {showSampleTree() && props.sampleTree !== null && hasSampleTreePathMeta() && props.sample && (
-              <div class="column is-6">
-                <h1 class="title is-5">Sample classification tree path</h1>
-                <DecisionTreePath
-                  decisionTree={props.sampleTree}
-                  path={getSampleTreePath(props.metadata.records, props.sample, props.record, props.consequenceId)}
-                />
-              </div>
-            )}
-          </div>
+        <div class="mt-3">
+          <h1 class="title is-5">
+            Consequence
+            <A href="#" onClick={toggleShowEmptyCsq} class="small-blue-link">
+              {showEmptyCsq() ? "(Hide empty fields)" : "(Show empty fields)"}
+            </A>
+          </h1>
+          <VariantConsequenceTable
+            variantType={props.variantType}
+            metadata={props.metadata}
+            record={props.record}
+            consequenceId={props.consequenceId}
+            isShowEmpty={showEmptyCsq()}
+          />
+        </div>
+        <div class="mt-3">
+          <h1 class="title is-5">Record</h1>
+          <VariantTable variant={props.record.data} />
+        </div>
+      </div>
+      <div class="column is-8">
+        <Show when={config().variant.samplesCells}>
+          {(samplesCells) => (
+            <div class="column">
+              <h1 class="title is-5">Samples</h1>
+              <VariantGenotypeTable
+                config={samplesCells()}
+                samples={samples()}
+                metadata={props.metadata}
+                variantType={props.variantType}
+                record={props.record}
+              />
+            </div>
+          )}
+        </Show>
+        <div class="columns mt-3">
+          {props.decisionTree !== null && hasDecisionTreePathMeta() && (
+            <div class="column is-6">
+              <h1 class="title is-5">Variant classification tree path</h1>
+              <DecisionTreePath
+                decisionTree={props.decisionTree}
+                path={getDecisionTreePath(props.metadata.records, props.record, props.consequenceId)}
+              />
+            </div>
+          )}
+          {showSampleTree() && props.sampleTree !== null && hasSampleTreePathMeta() && props.sample && (
+            <div class="column is-6">
+              <h1 class="title is-5">Sample classification tree path</h1>
+              <DecisionTreePath
+                decisionTree={props.sampleTree}
+                path={getSampleTreePath(props.metadata.records, props.sample, props.record, props.consequenceId)}
+              />
+            </div>
+          )}
         </div>
       </div>
-    </>
+    </div>
   );
 };

package/src/components/VariantConsequenceTable.tsx

@@ -1,4 +1,4 @@
-import { Component, For } from "solid-js";
+import { Component, For, Show } from "solid-js";
 import { VcfRecord } from "@molgenis/vip-report-vcf";
 import { Item } from "@molgenis/vip-report-api";
 import { Table } from "./Table.tsx";
@@ -6,12 +6,14 @@ import { initConfigCells } from "../utils/config/configCells.ts";
 import { RecordsTableCellLine, RecordsTableHeaderCell } from "./RecordsTable.tsx";
 import { VariantType } from "../utils/variantType.ts";
 import { MetadataContainer } from "../utils/api.ts";
+import { ConfigCellInfo } from "../types/configCells";
 
 export const VariantConsequenceTable: Component<{
   variantType: VariantType;
   metadata: MetadataContainer;
   record: Item<VcfRecord>;
   consequenceId: number;
+  isShowEmpty: boolean;
 }> = (props) => {
   const configCells = () =>
     initConfigCells(
@@ -26,21 +28,28 @@ export const VariantConsequenceTable: Component<{
       null,
     ).filter((configCell) => configCell.type !== "group");
 
+  function isEmptyValue(fieldConfig: ConfigCellInfo) {
+    const value = fieldConfig.value(props.record, props.consequenceId);
+    return value === null || value === undefined || (Array.isArray(value) && value.length === 0);
+  }
+
   return (
     <Table borderless={true}>
       <tbody>
-        <For each={configCells()}>
-          {(fieldConfig) => (
-            <tr>
-              <RecordsTableHeaderCell fieldConfig={fieldConfig} />
-              <td>
-                <RecordsTableCellLine
-                  fieldConfig={fieldConfig}
-                  record={props.record}
-                  valueIndex={props.consequenceId}
-                />
-              </td>
-            </tr>
+        <For each={configCells() as ConfigCellInfo[]}>
+          {(fieldConfig: ConfigCellInfo) => (
+            <Show when={!isEmptyValue(fieldConfig) || props.isShowEmpty}>
+              <tr>
+                <RecordsTableHeaderCell fieldConfig={fieldConfig} showParentHeader={true} />
+                <td>
+                  <RecordsTableCellLine
+                    fieldConfig={fieldConfig}
+                    record={props.record}
+                    valueIndex={props.consequenceId}
+                  />
+                </td>
+              </tr>
+            </Show>
           )}
         </For>
       </tbody>

package/src/components/VariantContainer.tsx

@@ -1,4 +1,4 @@
-import { Component, Show } from "solid-js";
+import { Component, createSignal, Show } from "solid-js";
 import { MetadataContainer, SampleContainer } from "../utils/api.ts";
 import { Item, Sample } from "@molgenis/vip-report-api";
 import { VcfRecord } from "@molgenis/vip-report-vcf";
@@ -11,6 +11,7 @@ import { VariantType } from "../utils/variantType.ts";
 import { getPedigreeSamples } from "../utils/sample.ts";
 import { VariantGenotypeTable } from "./VariantGenotypeTable.tsx";
 import { initConfig } from "../utils/config/config.ts";
+import { A } from "@solidjs/router";
 
 export const VariantContainer: Component<{
   config: ConfigJson;
@@ -21,6 +22,8 @@ export const VariantContainer: Component<{
 }> = (props) => {
   const config = () => initConfig(props.config, props.variantType, props.metadata, props.sample);
   const samples = (): Item<Sample>[] => (props.sample ? getPedigreeSamples(props.sample) : []);
+  const [showEmpty, setShowEmpty] = createSignal(false);
+  const toggleShowEmpty = () => setShowEmpty((isShow) => !isShow);
 
   return (
     <>
@@ -35,8 +38,18 @@ export const VariantContainer: Component<{
           <VariantTable variant={props.record.data} />
         </div>
         <div class="column is-3">
-          <h1 class="title is-5">Info</h1>
-          <VariantInfoTable variantType={props.variantType} metadata={props.metadata} record={props.record} />
+          <h1 class="title is-5">
+            Info
+            <A href="#" onClick={toggleShowEmpty} class="small-blue-link">
+              {showEmpty() ? "(Hide empty fields)" : "(Show empty fields)"}
+            </A>
+          </h1>
+          <VariantInfoTable
+            variantType={props.variantType}
+            metadata={props.metadata}
+            record={props.record}
+            isShowEmpty={showEmpty()}
+          />
         </div>
         <Show when={config().variant.samplesCells}>
           {(samplesCells) => (

package/src/components/VariantInfoTable.tsx

@@ -1,4 +1,4 @@
-import { Component, For } from "solid-js";
+import { Component, For, Show } from "solid-js";
 import { VcfRecord } from "@molgenis/vip-report-vcf";
 import { Table } from "./Table.tsx";
 import { Item } from "@molgenis/vip-report-api";
@@ -6,11 +6,13 @@ import { RecordsTableCell, RecordsTableHeaderCell } from "./RecordsTable.tsx";
 import { initConfigCells } from "../utils/config/configCells.ts";
 import { MetadataContainer } from "../utils/api.ts";
 import { VariantType } from "../utils/variantType.ts";
+import { ConfigCellInfo } from "../types/configCells";
 
 export const VariantInfoTable: Component<{
   variantType: VariantType;
   metadata: MetadataContainer;
   record: Item<VcfRecord>;
+  isShowEmpty: boolean;
 }> = (props) => {
   const configCells = () =>
     initConfigCells(
@@ -25,15 +27,22 @@ export const VariantInfoTable: Component<{
       null,
     ).filter((configCell) => configCell.type !== "group");
 
+  function isEmptyValue(fieldConfig: ConfigCellInfo) {
+    const value = props.record.data.n[fieldConfig.field.id];
+    return value === null || value === undefined || (Array.isArray(value) && value.length === 0);
+  }
+
   return (
     <Table borderless={true}>
       <tbody>
-        <For each={configCells()}>
-          {(fieldConfig) => (
-            <tr>
-              <RecordsTableHeaderCell fieldConfig={fieldConfig} showParentHeader={true} />
-              <RecordsTableCell fieldConfig={fieldConfig} record={props.record} />
-            </tr>
+        <For each={configCells() as ConfigCellInfo[]}>
+          {(fieldConfig: ConfigCellInfo) => (
+            <Show when={!isEmptyValue(fieldConfig) || props.isShowEmpty}>
+              <tr>
+                <RecordsTableHeaderCell fieldConfig={fieldConfig} showParentHeader={true} />
+                <RecordsTableCell fieldConfig={fieldConfig} record={props.record} />
+              </tr>
+            </Show>
           )}
         </For>
       </tbody>

package/src/components/field/info/FieldConsequence.tsx

@@ -1,15 +1,26 @@
-import { Component } from "solid-js";
+import { Component, Show } from "solid-js";
 import { Abbr } from "../../Abbr";
+import { ValueCategorical } from "../../../utils/vcf.ts";
 
-export const FieldConsequence: Component<{ value: string[] }> = (props) => {
+export const FieldConsequence: Component<{ value: ValueCategorical[] }> = (props) => {
   return (
-    <>
-      <span>{props.value[0]}</span>
-      {props.value.length > 1 && (
-        <span>
-          , <Abbr title={props.value.slice(1).join(", ")} value={"\u2026"} />
-        </span>
-      )}
-    </>
+    <Show when={props.value?.length > 0}>
+      <span>
+        {props.value[0]?.label}
+        {props.value.length > 1 && (
+          <>
+            ,{" "}
+            <Abbr
+              title={props.value
+                .slice(1)
+                .filter((csq) => csq !== null)
+                .map((csq) => csq.label)
+                .join(", ")}
+              value="…"
+            />
+          </>
+        )}
+      </span>
+    </Show>
   );
 };

package/src/mocks/GRCh38/field_metadata.json

@@ -126,6 +126,230 @@
           "numberCount": 1,
           "type": "FLOAT"
         },
+        "apogee_Score": {
+          "label": "Apogee score",
+          "description": "Apogee score for protein coding mtDNA variants",
+          "numberType": "NUMBER",
+          "numberCount": 1,
+          "type": "FLOAT"
+        },
+        "apogee_Uscore": {
+          "label": "Apogee unbiased score",
+          "description": "Apogee unbiased score for protein coding mtDNA variants",
+          "numberType": "NUMBER",
+          "numberCount": 1,
+          "type": "FLOAT"
+        },
+        "BIOTYPE": {
+          "label": "Biotype",
+          "description": "The Ensembl VEP Biotype.",
+          "numberType": "NUMBER",
+          "numberCount": 1,
+          "type": "CATEGORICAL",
+          "categories": {
+            "IG_C_gene": {
+              "label": "IG C gene"
+            },
+            "protein_coding_CDS_not_defined": {
+              "label": "protein coding CDS not defined"
+            },
+            "Mt_tRNA": {
+              "label": "Mt tRNA"
+            },
+            "TR_V_pseudogene": {
+              "label": "TR V pseudogene"
+            },
+            "other": {
+              "label": "other"
+            },
+            "vault_RNA": {
+              "label": "vault RNA"
+            },
+            "scRNA": {
+              "label": "scRNA"
+            },
+            "transcribed_pseudogene": {
+              "label": "transcribed pseudogene"
+            },
+            "lncRNA": {
+              "label": "lncRNA"
+            },
+            "IG_pseudogene": {
+              "label": "IG pseudogene"
+            },
+            "transcribed_unprocessed_pseudogene": {
+              "label": "transcribed unprocessed pseudogene"
+            },
+            "IG_V_pseudogene": {
+              "label": "IG V pseudogene"
+            },
+            "transcribed_unitary_pseudogene": {
+              "label": "transcribed unitary pseudogene"
+            },
+            "pseudogene": {
+              "label": "pseudogene"
+            },
+            "RNase_P_RNA": {
+              "label": "RNase P RNA"
+            },
+            "rRNA": {
+              "label": "rRNA"
+            },
+            "TR_V_gene": {
+              "label": "TR V gene"
+            },
+            "rRNA_pseudogene": {
+              "label": "rRNA pseudogene"
+            },
+            "TR_J_gene": {
+              "label": "TR J gene"
+            },
+            "aligned_transcript": {
+              "label": "aligned transcript"
+            },
+            "RNase_MRP_RNA": {
+              "label": "RNase MRP RNA"
+            },
+            "TR_D_gene": {
+              "label": "TR D gene"
+            },
+            "unprocessed_pseudogene": {
+              "label": "unprocessed pseudogene"
+            },
+            "IG_J_pseudogene": {
+              "label": "IG J pseudogene"
+            },
+            "processed_transcript": {
+              "label": "processed transcript"
+            },
+            "telomerase_RNA": {
+              "label": "telomerase RNA"
+            },
+            "protein_coding_LoF": {
+              "label": "protein coding LoF"
+            },
+            "ncRNA": {
+              "label": "ncRNA"
+            },
+            "TR_J_pseudogene": {
+              "label": "TR J pseudogene"
+            },
+            "retained_intron": {
+              "label": "retained intron"
+            },
+            "nonsense_mediated_decay": {
+              "label": "nonsense mediated decay"
+            },
+            "snRNA": {
+              "label": "snRNA"
+            },
+            "transcribed_processed_pseudogene": {
+              "label": "transcribed processed pseudogene"
+            },
+            "TR_C_gene": {
+              "label": "TR C gene"
+            },
+            "processed_pseudogene": {
+              "label": "processed pseudogene"
+            },
+            "translated_processed_pseudogene": {
+              "label": "translated processed pseudogene"
+            },
+            "miRNA": {
+              "label": "miRNA"
+            },
+            "protein_coding": {
+              "label": "protein coding"
+            },
+            "antisense_RNA": {
+              "label": "antisense RNA"
+            },
+            "IG_D_gene": {
+              "label": "IG D gene"
+            },
+            "LRG_gene": {
+              "label": "LRG gene"
+            },
+            "Mt_rRNA": {
+              "label": "Mt rRNA"
+            },
+            "mRNA": {
+              "label": "mRNA"
+            },
+            "ribozyme": {
+              "label": "ribozyme"
+            },
+            "unitary_pseudogene": {
+              "label": "unitary pseudogene"
+            },
+            "IG_J_gene": {
+              "label": "IG J gene"
+            },
+            "IG_V_gene": {
+              "label": "IG V gene"
+            },
+            "artifact": {
+              "label": "artifact"
+            },
+            "cdna_update": {
+              "label": "cdna update"
+            },
+            "ncRNA_pseudogene": {
+              "label": "ncRNA pseudogene"
+            },
+            "IG_C_pseudogene": {
+              "label": "IG C pseudogene"
+            },
+            "TEC": {
+              "label": "TEC"
+            },
+            "non_stop_decay": {
+              "label": "non stop decay"
+            },
+            "sRNA": {
+              "label": "sRNA"
+            },
+            "ccds_gene": {
+              "label": "ccds gene"
+            },
+            "tRNA": {
+              "label": "tRNA"
+            },
+            "snoRNA": {
+              "label": "snoRNA"
+            },
+            "scaRNA": {
+              "label": "scaRNA"
+            },
+            "misc_RNA": {
+              "label": "misc RNA"
+            },
+            "Y_RNA": {
+              "label": "Y RNA"
+            },
+            "promoter": {
+              "label": "promoter"
+            },
+            "promoter_flanking_region": {
+              "label": "promoter flanking region"
+            },
+            "enhancer": {
+              "label": "enhancer"
+            },
+            "CTCF_binding_site": {
+              "label": "CTCF binding site"
+            },
+            "open_chromatin_region": {
+              "label": "open chromatin region"
+            },
+            "TF_binding_site": {
+              "label": "transcription factor binding site"
+            },
+            "non_transcribed_region": {
+              "label": "non-transcribed region"
+            }
+          }
+        },
         "CAPICE_CL": {
           "label": "CAPICE",
           "description": "CAPICE classification",
@@ -323,7 +547,173 @@
           "description": "Effect(s) described as Sequence Ontology term(s)",
           "numberType": "OTHER",
           "separator": "&",
-          "type": "STRING"
+          "type": "CATEGORICAL",
+          "categories": {
+            "transcript_ablation": {
+              "label": "transcript ablation",
+              "description": "A feature ablation whereby the deleted region includes a transcript feature"
+            },
+            "splice_acceptor_variant": {
+              "label": "splice acceptor variant",
+              "description": "A splice variant that changes the 2 base region at the 3' end of an intron"
+            },
+            "splice_donor_variant": {
+              "label": "splice donor variant",
+              "description": "A splice variant that changes the 2 base region at the 5' end of an intron"
+            },
+            "stop_gained": {
+              "label": "stop gained",
+              "description": "A sequence variant whereby at least one base of a codon is changed, resulting in a premature stop codon, leading to a shortened transcript"
+            },
+            "frameshift_variant": {
+              "label": "frameshift variant",
+              "description": "A sequence variant which causes a disruption of the translational reading frame, because the number of nucleotides inserted or deleted is not a multiple of three"
+            },
+            "stop_lost": {
+              "label": "stop lost",
+              "description": "A sequence variant where at least one base of the terminator codon (stop) is changed, resulting in an elongated transcript"
+            },
+            "start_lost": {
+              "label": "start lost",
+              "description": "A codon variant that changes at least one base of the canonical start codon"
+            },
+            "transcript_amplification": {
+              "label": "transcript amplification",
+              "description": "A feature amplification of a region containing a transcript"
+            },
+            "feature_elongation": {
+              "label": "feature elongation",
+              "description": "A sequence variant that causes the extension of a genomic feature, with regard to the reference sequence"
+            },
+            "feature_truncation": {
+              "label": "feature truncation",
+              "description": "A sequence variant that causes the reduction of a genomic feature, with regard to the reference sequence"
+            },
+            "inframe_insertion": {
+              "label": "inframe insertion",
+              "description": "An inframe non synonymous variant that inserts bases into in the coding sequence"
+            },
+            "inframe_deletion": {
+              "label": "inframe deletion",
+              "description": "An inframe non synonymous variant that deletes bases from the coding sequence"
+            },
+            "missense_variant": {
+              "label": "missense variant",
+              "description": "A sequence variant, that changes one or more bases, resulting in a different amino acid sequence but where the length is preserved"
+            },
+            "protein_altering_variant": {
+              "label": "protein altering variant",
+              "description": "A sequence_variant which is predicted to change the protein encoded in the coding sequence"
+            },
+            "splice_donor_5th_base_variant": {
+              "label": "splice donor 5th base variant",
+              "description": "A sequence variant that causes a change at the 5th base pair after the start of the intron in the orientation of the transcript"
+            },
+            "splice_region_variant": {
+              "label": "splice region variant",
+              "description": "A sequence variant in which a change has occurred within the region of the splice site, either within 1-3 bases of the exon or 3-8 bases of the intron"
+            },
+            "splice_donor_region_variant": {
+              "label": "splice donor region variant",
+              "description": "A sequence variant that falls in the region between the 3rd and 6th base after splice junction (5' end of intron)"
+            },
+            "splice_polypyrimidine_tract_variant": {
+              "label": "splice polypyrimidine tract variant",
+              "description": "A sequence variant that falls in the polypyrimidine tract at 3' end of intron between 17 and 3 bases from the end (acceptor -3 to acceptor -17)"
+            },
+            "incomplete_terminal_codon_variant": {
+              "label": "incomplete terminal codon variant",
+              "description": "A sequence variant where at least one base of the final codon of an incompletely annotated transcript is changed"
+            },
+            "start_retained_variant": {
+              "label": "start retained variant",
+              "description": "A sequence variant where at least one base in the start codon is changed, but the start remains"
+            },
+            "stop_retained_variant": {
+              "label": "stop retained variant",
+              "description": "A sequence variant where at least one base in the terminator codon is changed, but the terminator remains"
+            },
+            "synonymous_variant": {
+              "label": "synonymous variant",
+              "description": "A sequence variant where there is no resulting change to the encoded amino acid"
+            },
+            "coding_sequence_variant": {
+              "label": "coding sequence variant",
+              "description": "A sequence variant that changes the coding sequence"
+            },
+            "mature_miRNA_variant": {
+              "label": "mature miRNA variant",
+              "description": "A transcript variant located with the sequence of the mature miRNA"
+            },
+            "5_prime_UTR_variant": {
+              "label": "5 prime UTR variant",
+              "description": "A UTR variant of the 5' UTR"
+            },
+            "3_prime_UTR_variant": {
+              "label": "3 prime UTR variant",
+              "description": "A UTR variant of the 3' UTR"
+            },
+            "non_coding_transcript_exon_variant": {
+              "label": "non coding transcript exon variant",
+              "description": "A sequence variant that changes non-coding exon sequence in a non-coding transcript"
+            },
+            "intron_variant": {
+              "label": "intron variant",
+              "description": "A transcript variant occurring within an intron"
+            },
+            "NMD_transcript_variant": {
+              "label": "NMD transcript variant",
+              "description": "A variant in a transcript that is the target of NMD"
+            },
+            "non_coding_transcript_variant": {
+              "label": "non coding transcript variant",
+              "description": "A transcript variant of a non coding RNA gene"
+            },
+            "coding_transcript_variant": {
+              "label": "coding transcript variant",
+              "description": "A transcript variant of a protein coding gene"
+            },
+            "upstream_gene_variant": {
+              "label": "upstream gene variant",
+              "description": "A sequence variant located 5' of a gene"
+            },
+            "downstream_gene_variant": {
+              "label": "downstream gene variant",
+              "description": "A sequence variant located 3' of a gene"
+            },
+            "TFBS_ablation": {
+              "label": "TFBS ablation",
+              "description": "A feature ablation whereby the deleted region includes a transcription factor binding site"
+            },
+            "TFBS_amplification": {
+              "label": "TFBS amplification",
+              "description": "A feature amplification of a region containing a transcription factor binding site"
+            },
+            "TF_binding_site_variant": {
+              "label": "TF binding site variant",
+              "description": "A sequence variant located within a transcription factor binding site"
+            },
+            "regulatory_region_ablation": {
+              "label": "regulatory region ablation",
+              "description": "A feature ablation whereby the deleted region includes a regulatory region"
+            },
+            "regulatory_region_amplification": {
+              "label": "regulatory region amplification",
+              "description": "A feature amplification of a region containing a regulatory region"
+            },
+            "regulatory_region_variant": {
+              "label": "regulatory region variant",
+              "description": "A sequence variant located within a regulatory region"
+            },
+            "intergenic_variant": {
+              "label": "intergenic variant",
+              "description": "A sequence variant located in the intergenic region, between genes"
+            },
+            "sequence_variant": {
+              "label": "sequence variant",
+              "description": "A sequence_variant is a non exact copy of a sequence_feature or genome exhibiting one or more sequence_alteration"
+            }
+          }
         },
         "Existing_variation": {
           "label": "Ex. var.",
@@ -509,6 +899,13 @@
           "numberCount": 1,
           "type": "STRING"
         },
+        "hmtvar_DiseaseScore": {
+          "label": "HmtVar disease score",
+          "description": "HmtVar disease score for mtDNA tRNA variants",
+          "numberType": "NUMBER",
+          "numberCount": 1,
+          "type": "FLOAT"
+        },
         "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",
@@ -599,6 +996,20 @@
             }
           }
         },
+        "mitoTip_Quartile": {
+          "label": "MitoTIP Quartile",
+          "description": "MitoTIP score quartile",
+          "numberType": "NUMBER",
+          "numberCount": 1,
+          "type": "STRING"
+        },
+        "mitoTip_Score": {
+          "label": "MitoTip Score",
+          "description": "MitoTIP score for mtDNA tRNA variants",
+          "numberType": "NUMBER",
+          "numberCount": 1,
+          "type": "FLOAT"
+        },
         "ncER": {
           "label": "ncER",
           "description": "Non-coding essential regulation, from: 0(probably not essential for regulation) to 100 (probably essential for regulation).",
@@ -704,6 +1115,19 @@
           "numberCount": 1,
           "type": "STRING"
         },
+        "SYMBOL_SOURCE": {
+          "label": "Symbol Source",
+          "description": "The source of the symbol.",
+          "numberType": "NUMBER",
+          "numberCount": 1,
+          "type": "CATEGORICAL",
+          "categories": {
+            "EntrezGene": {
+              "label": "EntrezGene",
+              "description": "Symbol source Entrez Gene"
+            }
+          }
+        },
         "VIPP": {
           "label": "VIP path",
           "description": "VIP decision tree path",

package/src/mocks/GRCh38/vcf/samples_1.vcf

@@ -14,7 +14,6 @@
 ##INFO=<ID=MATE_BND_DEPTH,Number=1,Type=Integer,Description="Read depth at remote translocation mate breakend">
 ##INFO=<ID=ReverseComplementedAlleles,Number=0,Type=Flag,Description="The REF and the ALT alleles have been reverse complemented in liftover since the mapping from the previous reference to the current one was on the negative strand.">
 ##INFO=<ID=SVLEN,Number=.,Type=Integer,Description="Difference in length between REF and ALT alleles">
-##INFO=<ID=SVTYPE,Number=1,Type=String,Description="Type of structural variant">
 ##INFO=<ID=SwappedAlleles,Number=0,Type=Flag,Description="The REF and the ALT alleles have been swapped in liftover due to changes in the reference. It is possible that not all INFO annotations reflect this swap, and in the genotypes, only the GT:VIPC_S, PL, and AD fields have been modified. You should check the TAGS_TO_REVERSE parameter that was used during the LiftOver to be sure.">
 ##INFO=<ID=gnomAD,Number=.,Type=String,Description="/groups/solve-rd/tmp10/vip/resources/GRCh38/gnomad.genomes.v3.1.2.sites.stripped.vcf.gz (exact)">
 ##INFO=<ID=gnomAD_AF,Number=.,Type=String,Description="AF field from /groups/solve-rd/tmp10/vip/resources/GRCh38/gnomad.genomes.v3.1.2.sites.stripped.vcf.gz">
@@ -242,16 +241,11 @@ chr1	9982480	.	C	T	.	PASS	CSQ=T|missense_variant|MODERATE|NMNAT1|64802|Transcrip
 chr1	16049917	n_alt	G	N	.	PASS	CSQ=N|splice_donor_variant|HIGH|CLCNKB|1188|Transcript|NM_000085.5|protein_coding||10/19||||||||CS1211892&CS971662|1||1||1|EntrezGene||||||||||1&1|||||||||||||||||VUS|0.45317215|HP:0000951||AR||||||||P|filter&vkgl&clinVar&gnomad&effect&spliceAI&annotSV&impact&exit_p|,N|splice_donor_variant|HIGH|CLCNKB|1188|Transcript|NM_001165945.2|protein_coding||3/12||||||||CS1211892&CS971662|1||1|||EntrezGene||||||||||1&1|||||||||||||||||VUS|0.45317215|HP:0000951||AR||||||||P|filter&vkgl&clinVar&gnomad&effect&spliceAI&annotSV&impact&exit_p|	GT:VIPC_S	1|1:U1
 chr1	17022724	n_ref	N	A	.	PASS	CSQ=A|coding_sequence_variant|MODIFIER|SDHB|6390|Transcript|NM_003000.3|protein_coding|7/8||NM_003000.3:c.649C>T||662/1015|649/843|217/280||Ngc/Tgc|CM1210440&CM094752|1||-1||1|EntrezGene||||||||||1&1|||||||||||||||||VUS|0.20536129|HP:0000951||AD&AR||||||||P|filter&vkgl&clinVar&gnomad&effect&spliceAI&annotSV&impact&exit_p|	GT:VIPC_S	1/0:U1
 chr1	17022724	g_ref	G	A	.	PASS	CSQ=A|missense_variant|MODERATE|SDHB|6390|Transcript|NM_003000.3|protein_coding|7/8||NM_003000.3:c.649C>T|NP_002991.2:p.Arg217Cys|662/1015|649/843|217/280|R/C|Cgc/Tgc|rs200245469&CM1210440&CM094752|1||-1||1|EntrezGene|||||0|1||pathogenic&likely_pathogenic||1&1&1||||||||28|6|6|5|0.00|0.00|0.00|0.00|SDHB|VUS|0.88626856|HP:0000951||AD&AR|LP||||chr1:17022724-17022724|6.57186e-06|0|P|filter&vkgl&exit_p|	GT:VIPC_S	1/0:U1
-chr1	152548312	symbolic1	A	<DEL>	.	PASS	CSQ=deletion|transcript_ablation|HIGH|LCE3D|84648|Transcript|NM_032563.2|protein_coding|||||||||||1||-1||1|EntrezGene|||||||||||||||||||||||||||||||||||||||P|filter&vkgl&clinVar&gnomad&effect&spliceAI&annotSV&impact&exit_p|,deletion|upstream_gene_variant|MODIFIER|LCE3C|353144|Transcript|NM_178434.3|protein_coding|||||||||||1|2608|1|||EntrezGene|||||||||||||||||||||||||||||||||||||||P|filter&vkgl&clinVar&gnomad&effect&spliceAI&annotSV&impact&exit_p|,deletion|transcript_ablation|HIGH|LCE3E|353145|Transcript|NM_178435.4|protein_coding|||||||||||1||-1|||EntrezGene|||||||||||||||||||||||||||||||||||||||P|filter&vkgl&clinVar&gnomad&effect&spliceAI&annotSV&impact&exit_p|,deletion|regulatory_region_ablation&regulatory_region_variant|MODIFIER|||RegulatoryFeature|ENSR00000372937||||||||||||1||||||||||||||||||||||||||||||||||||||||||||P|filter&vkgl&clinVar&gnomad&effect&spliceAI&annotSV&impact&exit_p|,deletion|regulatory_region_ablation&regulatory_region_variant|MODIFIER|||RegulatoryFeature|ENSR00000013752||||||||||||1||||||||||||||||||||||||||||||||||||||||||||P|filter&vkgl&clinVar&gnomad&effect&spliceAI&annotSV&impact&exit_p|,deletion|regulatory_region_ablation&regulatory_region_variant|MODIFIER|||RegulatoryFeature|ENSR00000372939||||||||||||1||||||||||||||||||||||||||||||||||||||||||||P|filter&vkgl&clinVar&gnomad&effect&spliceAI&annotSV&impact&exit_p|,deletion|regulatory_region_ablation&regulatory_region_variant|MODIFIER|||RegulatoryFeature|ENSR00000372940||||||||||||1||||||||||||||||||||||||||||||||||||||||||||P|filter&vkgl&clinVar&gnomad&effect&spliceAI&annotSV&impact&exit_p|,deletion|regulatory_region_ablation&regulatory_region_variant|MODIFIER|||RegulatoryFeature|ENSR00001171682||||||||||||1||||||||||||||||||||||||||||||||||||||||||||P|filter&vkgl&clinVar&gnomad&effect&spliceAI&annotSV&impact&exit_p|,deletion|regulatory_region_ablation&regulatory_region_variant|MODIFIER|||RegulatoryFeature|ENSR00000254476||||||||||||1||||||||||||||||||||||||||||||||||||||||||||P|filter&vkgl&clinVar&gnomad&effect&spliceAI&annotSV&impact&exit_p|,deletion|regulatory_region_ablation&regulatory_region_variant|MODIFIER|||RegulatoryFeature|ENSR00000931036||||||||||||1||||||||||||||||||||||||||||||||||||||||||||P|filter&vkgl&clinVar&gnomad&effect&spliceAI&annotSV&impact&exit_p|,deletion|regulatory_region_ablation&regulatory_region_variant|MODIFIER|||RegulatoryFeature|ENSR00001171683||||||||||||1||||||||||||||||||||||||||||||||||||||||||||P|filter&vkgl&clinVar&gnomad&effect&spliceAI&annotSV&impact&exit_p|,deletion|TFBS_ablation&TF_binding_site_variant|MODERATE|||MotifFeature|ENSM00191731851||||||||||||1||||||||||||||||||||||||||||||||||||||||||||P|filter&vkgl&clinVar&gnomad&effect&spliceAI&annotSV&impact&exit_p|,deletion|TFBS_ablation&TF_binding_site_variant|MODERATE|||MotifFeature|ENSM00189591243||||||||||||1||||||||||||||||||||||||||||||||||||||||||||P|filter&vkgl&clinVar&gnomad&effect&spliceAI&annotSV&impact&exit_p|,deletion|TFBS_ablation&TF_binding_site_variant|MODERATE|||MotifFeature|ENSM00078414360||||||||||||1||||||||||||||||||||||||||||||||||||||||||||P|filter&vkgl&clinVar&gnomad&effect&spliceAI&annotSV&impact&exit_p|,deletion|TFBS_ablation&TF_binding_site_variant|MODERATE|||MotifFeature|ENSM00078058090||||||||||||1||||||||||||||||||||||||||||||||||||||||||||P|filter&vkgl&clinVar&gnomad&effect&spliceAI&annotSV&impact&exit_p|,deletion|TFBS_ablation&TF_binding_site_variant|MODERATE|||MotifFeature|ENSM00000257725||||||||||||1||||||||||||||||||||||||||||||||||||||||||||P|filter&vkgl&clinVar&gnomad&effect&spliceAI&annotSV&impact&exit_p|;SVLEN=-49314;SVTYPE=DEL	GT:VIPC_S	1|1:U1
-chr2	47408528	symbolic2	G	<INS>	.	PASS	CSQ=insertion|splice_polypyrimidine_tract_variant&coding_sequence_variant&intron_variant&feature_elongation|LOW|MSH2|4436|Transcript|NM_000251.3|protein_coding|2-8/16|2-8/15|||376-?/3115|340-?/2805|114-?/934||||1||1||1|EntrezGene|||||||||||||||||||||||||||||||||||||||P|filter&vkgl&clinVar&gnomad&effect&spliceAI&annotSV&impact&exit_p|,insertion|splice_polypyrimidine_tract_variant&coding_sequence_variant&intron_variant&feature_elongation|LOW|MSH2|4436|Transcript|NM_001258281.1|protein_coding|3-9/17|3-9/16|||281-?/3025|142-?/2607|48-?/868||||1||1|||EntrezGene|||||||||||||||||||||||||||||||||||||||P|filter&vkgl&clinVar&gnomad&effect&spliceAI&annotSV&impact&exit_p|,insertion|regulatory_region_variant|MODIFIER|||RegulatoryFeature|ENSR00001031132||||||||||||1||||||||||||||||||||||||||||||||||||||||||||P|filter&vkgl&clinVar&gnomad&effect&spliceAI&annotSV&impact&exit_p|,insertion|regulatory_region_variant|MODIFIER|||RegulatoryFeature|ENSR00000605106||||||||||||1||||||||||||||||||||||||||||||||||||||||||||P|filter&vkgl&clinVar&gnomad&effect&spliceAI&annotSV&impact&exit_p|,insertion|regulatory_region_variant|MODIFIER|||RegulatoryFeature|ENSR00001031134||||||||||||1||||||||||||||||||||||||||||||||||||||||||||P|filter&vkgl&clinVar&gnomad&effect&spliceAI&annotSV&impact&exit_p|,insertion|regulatory_region_variant|MODIFIER|||RegulatoryFeature|ENSR00000605107||||||||||||1||||||||||||||||||||||||||||||||||||||||||||P|filter&vkgl&clinVar&gnomad&effect&spliceAI&annotSV&impact&exit_p|,insertion|regulatory_region_variant|MODIFIER|||RegulatoryFeature|ENSR00000605109||||||||||||1||||||||||||||||||||||||||||||||||||||||||||P|filter&vkgl&clinVar&gnomad&effect&spliceAI&annotSV&impact&exit_p|,insertion|regulatory_region_variant|MODIFIER|||RegulatoryFeature|ENSR00001031136||||||||||||1||||||||||||||||||||||||||||||||||||||||||||P|filter&vkgl&clinVar&gnomad&effect&spliceAI&annotSV&impact&exit_p|,insertion|regulatory_region_variant|MODIFIER|||RegulatoryFeature|ENSR00000605111||||||||||||1||||||||||||||||||||||||||||||||||||||||||||P|filter&vkgl&clinVar&gnomad&effect&spliceAI&annotSV&impact&exit_p|,insertion|TF_binding_site_variant|MODIFIER|||MotifFeature|ENSM00526224866||||||||||||1||||||||||||||||||||||||||||||||||||||||||||P|filter&vkgl&clinVar&gnomad&effect&spliceAI&annotSV&impact&exit_p|,insertion|TF_binding_site_variant|MODIFIER|||MotifFeature|ENSM00200869503||||||||||||1||||||||||||||||||||||||||||||||||||||||||||P|filter&vkgl&clinVar&gnomad&effect&spliceAI&annotSV&impact&exit_p|,insertion|TF_binding_site_variant|MODIFIER|||MotifFeature|ENSM00037157434||||||||||||1||||||||||||||||||||||||||||||||||||||||||||P|filter&vkgl&clinVar&gnomad&effect&spliceAI&annotSV&impact&exit_p|,insertion|TF_binding_site_variant|MODIFIER|||MotifFeature|ENSM00211420385||||||||||||1||||||||||||||||||||||||||||||||||||||||||||P|filter&vkgl&clinVar&gnomad&effect&spliceAI&annotSV&impact&exit_p|,insertion|TF_binding_site_variant|MODIFIER|||MotifFeature|ENSM00211397893||||||||||||1||||||||||||||||||||||||||||||||||||||||||||P|filter&vkgl&clinVar&gnomad&effect&spliceAI&annotSV&impact&exit_p|,insertion|TF_binding_site_variant|MODIFIER|||MotifFeature|ENSM00191281526||||||||||||1||||||||||||||||||||||||||||||||||||||||||||P|filter&vkgl&clinVar&gnomad&effect&spliceAI&annotSV&impact&exit_p|,insertion|TF_binding_site_variant|MODIFIER|||MotifFeature|ENSM00524206131||||||||||||1||||||||||||||||||||||||||||||||||||||||||||P|filter&vkgl&clinVar&gnomad&effect&spliceAI&annotSV&impact&exit_p|,insertion|TF_binding_site_variant|MODIFIER|||MotifFeature|ENSM00191128737||||||||||||1||||||||||||||||||||||||||||||||||||||||||||P|filter&vkgl&clinVar&gnomad&effect&spliceAI&annotSV&impact&exit_p|,insertion|TF_binding_site_variant|MODIFIER|||MotifFeature|ENSM00523779682||||||||||||1||||||||||||||||||||||||||||||||||||||||||||P|filter&vkgl&clinVar&gnomad&effect&spliceAI&annotSV&impact&exit_p|,insertion|TF_binding_site_variant|MODIFIER|||MotifFeature|ENSM00523716616||||||||||||1||||||||||||||||||||||||||||||||||||||||||||P|filter&vkgl&clinVar&gnomad&effect&spliceAI&annotSV&impact&exit_p|,insertion|TF_binding_site_variant|MODIFIER|||MotifFeature|ENSM00524736808||||||||||||1||||||||||||||||||||||||||||||||||||||||||||P|filter&vkgl&clinVar&gnomad&effect&spliceAI&annotSV&impact&exit_p|,insertion|TF_binding_site_variant|MODIFIER|||MotifFeature|ENSM00522488084||||||||||||1||||||||||||||||||||||||||||||||||||||||||||P|filter&vkgl&clinVar&gnomad&effect&spliceAI&annotSV&impact&exit_p|,insertion|TF_binding_site_variant|MODIFIER|||MotifFeature|ENSM00522348227||||||||||||1||||||||||||||||||||||||||||||||||||||||||||P|filter&vkgl&clinVar&gnomad&effect&spliceAI&annotSV&impact&exit_p|,insertion|TF_binding_site_variant|MODIFIER|||MotifFeature|ENSM00189912570||||||||||||1||||||||||||||||||||||||||||||||||||||||||||P|filter&vkgl&clinVar&gnomad&effect&spliceAI&annotSV&impact&exit_p|,insertion|TF_binding_site_variant|MODIFIER|||MotifFeature|ENSM00151154280||||||||||||1||||||||||||||||||||||||||||||||||||||||||||P|filter&vkgl&clinVar&gnomad&effect&spliceAI&annotSV&impact&exit_p|,insertion|TF_binding_site_variant|MODIFIER|||MotifFeature|ENSM00521803756||||||||||||1||||||||||||||||||||||||||||||||||||||||||||P|filter&vkgl&clinVar&gnomad&effect&spliceAI&annotSV&impact&exit_p|,insertion|TF_binding_site_variant|MODIFIER|||MotifFeature|ENSM00525714757||||||||||||1||||||||||||||||||||||||||||||||||||||||||||P|filter&vkgl&clinVar&gnomad&effect&spliceAI&annotSV&impact&exit_p|,insertion|TF_binding_site_variant|MODIFIER|||MotifFeature|ENSM00522888937||||||||||||1||||||||||||||||||||||||||||||||||||||||||||P|filter&vkgl&clinVar&gnomad&effect&spliceAI&annotSV&impact&exit_p|,insertion|TF_binding_site_variant|MODIFIER|||MotifFeature|ENSM00003947213||||||||||||1||||||||||||||||||||||||||||||||||||||||||||P|filter&vkgl&clinVar&gnomad&effect&spliceAI&annotSV&impact&exit_p|,insertion|TF_binding_site_variant|MODIFIER|||MotifFeature|ENSM00190965228||||||||||||1||||||||||||||||||||||||||||||||||||||||||||P|filter&vkgl&clinVar&gnomad&effect&spliceAI&annotSV&impact&exit_p|,insertion|TF_binding_site_variant|MODIFIER|||MotifFeature|ENSM00189989760||||||||||||1||||||||||||||||||||||||||||||||||||||||||||P|filter&vkgl&clinVar&gnomad&effect&spliceAI&annotSV&impact&exit_p|,insertion|TF_binding_site_variant|MODIFIER|||MotifFeature|ENSM00190028111||||||||||||1||||||||||||||||||||||||||||||||||||||||||||P|filter&vkgl&clinVar&gnomad&effect&spliceAI&annotSV&impact&exit_p|,insertion|TF_binding_site_variant|MODIFIER|||MotifFeature|ENSM00525662463||||||||||||1||||||||||||||||||||||||||||||||||||||||||||P|filter&vkgl&clinVar&gnomad&effect&spliceAI&annotSV&impact&exit_p|,insertion|TF_binding_site_variant|MODIFIER|||MotifFeature|ENSM00190489771||||||||||||1||||||||||||||||||||||||||||||||||||||||||||P|filter&vkgl&clinVar&gnomad&effect&spliceAI&annotSV&impact&exit_p|,insertion|TF_binding_site_variant|MODIFIER|||MotifFeature|ENSM00524615628||||||||||||1||||||||||||||||||||||||||||||||||||||||||||P|filter&vkgl&clinVar&gnomad&effect&spliceAI&annotSV&impact&exit_p|,insertion|TF_binding_site_variant|MODIFIER|||MotifFeature|ENSM00000366692||||||||||||1||||||||||||||||||||||||||||||||||||||||||||P|filter&vkgl&clinVar&gnomad&effect&spliceAI&annotSV&impact&exit_p|,insertion|TF_binding_site_variant|MODIFIER|||MotifFeature|ENSM00208026052||||||||||||1||||||||||||||||||||||||||||||||||||||||||||P|filter&vkgl&clinVar&gnomad&effect&spliceAI&annotSV&impact&exit_p|;SVLEN=-49314;SVTYPE=INS	GT:VIPC_S	0|0:U1
 chr4	105399137	.	G	A	.	PASS	CSQ=A|missense_variant|MODERATE|PPA2|27068|Transcript|NM_006903.4|protein_coding|7/11||NM_006903.4:c.596C>T|NP_008834.3:p.Pro199Leu|616/1586|596/918|199/305|P/L|cCg/cTg|rs138215926&CM1610192|1||-1|||EntrezGene|||||0|0.985||pathogenic||1&1||||||||-34|27|-2|-43|0.00|0.00|0.00|0.00|PPA2|VUS|0.79802734|||AR|LP||||chr4:105399137-105399137|0.000434159|0|P|filter&vkgl&exit_p|,A|missense_variant|MODERATE|PPA2|27068|Transcript|NM_176866.2|protein_coding|4/8||NM_176866.2:c.377C>T|NP_789842.2:p.Pro126Leu|397/1367|377/699|126/232|P/L|cCg/cTg|rs138215926&CM1610192|1||-1|||EntrezGene|||||0|0.992||pathogenic||1&1||||||||-34|27|-2|-43|0.00|0.00|0.00|0.00|PPA2|VUS|0.76154137|||AR|LP||||chr4:105399137-105399137|0.000434159|0|P|filter&vkgl&exit_p|,A|missense_variant|MODERATE|PPA2|27068|Transcript|NM_176867.3|protein_coding|2/6||NM_176867.3:c.185C>T|NP_789843.2:p.Pro62Leu|205/1175|185/507|62/168|P/L|cCg/cTg|rs138215926&CM1610192|1||-1|||EntrezGene|||||0|0.995||pathogenic||1&1||||||||-34|27|-2|-43|0.00|0.00|0.00|0.00|PPA2|VUS|0.7596747|||AR|LP||||chr4:105399137-105399137|0.000434159|0|P|filter&vkgl&exit_p|,A|missense_variant|MODERATE|PPA2|27068|Transcript|NM_176869.3|protein_coding|8/12||NM_176869.3:c.683C>T|NP_789845.1:p.Pro228Leu|695/1665|683/1005|228/334|P/L|cCg/cTg|rs138215926&CM1610192|1||-1||1|EntrezGene|||||0|0.993||pathogenic||1&1||||||||-34|27|-2|-43|0.00|0.00|0.00|0.00|PPA2|VUS|0.7574089|||AR|LP||||chr4:105399137-105399137|0.000434159|0|P|filter&vkgl&exit_p|,A|regulatory_region_variant|MODIFIER|||RegulatoryFeature|ENSR00001252884|enhancer||||||||||rs138215926&CM1610192|1|||||||||||||pathogenic||1&1||||||||||||||||||||||||||chr4:105399137-105399137|0.000434159|0|P|filter&vkgl&clinVar&exit_p|	GT:VIPC_S	0/0:U1
-chr7	41977712	single_breakend_nation	C	C.	.	PASS	CSQ=BND|coding_sequence_variant|MODIFIER|GLI3|2737|Transcript|NM_000168.6|protein_coding|12/15||||1938/8405|1657/4743|553/1580||||1||-1||1|EntrezGene|||||||||||||||||||||||||||||||||||||||P|filter&vkgl&clinVar&gnomad&effect&spliceAI&annotSV&impact&exit_p|,BND|regulatory_region_variant|MODIFIER|||RegulatoryFeature|ENSR00000823237||||||||||||1||||||||||||||||||||||||||||||||||||||||||||P|filter&vkgl&clinVar&gnomad&effect&spliceAI&annotSV&impact&exit_p|,BND|regulatory_region_variant|MODIFIER|||RegulatoryFeature|ENSR00000325885||||||||||||1||||||||||||||||||||||||||||||||||||||||||||P|filter&vkgl&clinVar&gnomad&effect&spliceAI&annotSV&impact&exit_p|;SVTYPE=BND	GT:VIPC_S	0/1:U1
 chr7	42025358	.	GACTC	G	.	PASS	CSQ=-|frameshift_variant|HIGH|GLI3|2737|Transcript|NM_000168.6|protein_coding|9/15||NM_000168.6:c.1258_1261del|NP_000159.3:p.Glu420LeufsTer3|1539-1542/8405|1258-1261/4743|420-421/1580|ES/X|GAGTct/ct||1||-1||1|EntrezGene||||||||||||||||||18|21|-40|6|0.00|0.00|0.00|0.00|GLI3|VUS|0.98730624||1|AD|LP|||||||P|filter&vkgl&exit_p|	GT:VIPC_S	0/1:U1
-chr8	60852584	breakend1	G	]11:134014225]G	.	PASS	BND_DEPTH=26;CSQ=BND|intron_variant|MODIFIER|CHD7|55636|Transcript|NM_001316690.1|protein_coding||2/4|||||||||1||1|||EntrezGene|||||||||||||||||||||||||||||||||||||||P|filter&vkgl&clinVar&gnomad&effect&spliceAI&annotSV&impact&exit_p|,BND|coding_sequence_variant|MODIFIER|CHD7|55636|Transcript|NM_017780.4|protein_coding|30/38||||6499/11606|5982/8994|1994/2997||||1||1||1|EntrezGene|||||||||||||||||||||||||||||||||||||||P|filter&vkgl&clinVar&gnomad&effect&spliceAI&annotSV&impact&exit_p|,BND|regulatory_region_variant|MODIFIER|||RegulatoryFeature|ENSR00001138764||||||||||||1||||||||||||||||||||||||||||||||||||||||||||P|filter&vkgl&clinVar&gnomad&effect&spliceAI&annotSV&impact&exit_p|;MATEID=breakend2;MATE_BND_DEPTH=39;SVTYPE=BND	GT:VIPC_S	0/0:U1
 chr8	144085597	.	CAG	C	.	PASS	CSQ=-|frameshift_variant|HIGH|GPAA1|8733|Transcript|NM_003801.4|protein_coding|11/12||NM_003801.4:c.1477_1478del|NP_003792.1:p.Arg493GlyfsTer152|1574-1575/2054|1477-1478/1866|493/621|R/X|AGg/g|rs782339984|1||1||1|EntrezGene||||||||pathogenic||1||||||||-15|-8|12|-21|0.02|0.00|0.00|0.00|GPAA1|VUS|0.99313146|||AR|LP||||chr8:144085598-144085600|0.000144549|0|P|filter&vkgl&exit_p|,-|downstream_gene_variant|MODIFIER|EXOSC4|54512|Transcript|NM_019037.3|protein_coding||||||||||rs782339984|1|4950|1|||EntrezGene||||||||pathogenic||1||||||||-15|-8|12|-21|0.02|0.00|0.00|0.00|GPAA1|VUS|0.0936931||||||||chr8:144085598-144085600|0.000144549|0|P|filter&vkgl&clinVar&exit_p|	GT:VIPC_S	1|1:U1
 chr9	104784352	.	AAAGAT	A	.	PASS	CSQ=-|frameshift_variant|HIGH|ABCA1|19|Transcript|NM_005502.4|protein_coding|50/50||NM_005502.4:c.6744_6748del|NP_005493.2:p.Phe2250ThrfsTer3|7057-7061/10408|6744-6748/6786|2248-2250/2261|TSF/TX|acATCTTtt/actt||1||-1||1|EntrezGene|||||||||||||||||||||||||||VUS|0.983508|HP:0000951||AD&AR||||||||P|filter&vkgl&clinVar&gnomad&effect&spliceAI&annotSV&impact&exit_p|,-|regulatory_region_variant|MODIFIER|||RegulatoryFeature|ENSR00000889339|promoter_flanking_region|||||||||||1||||||||||||||||||||||||||||||||||||||||||||P|filter&vkgl&clinVar&gnomad&effect&spliceAI&annotSV&impact&exit_p|	GT:VIPC_S	0/1:U1
 chr10	124402930	.	G	C	.	PASS	CSQ=C|stop_gained|HIGH|OAT|4942|Transcript|NM_000274.4|protein_coding|7/10||NM_000274.4:c.897C>G|NP_000265.1:p.Tyr299Ter|977/2039|897/1320|299/439|Y/*|taC/taG|rs121965057&CM920525|1||-1||1|EntrezGene||||||||likely_pathogenic&pathogenic||1&1|1737786&23076989&1609808&22674428|||||||-1|-3|-3|4|0.00|0.00|0.00|0.00|OAT|VUS|0.98058724|||AR|LP||||chr10:124402930-124402930|2.6295e-05|0|P|filter&vkgl&exit_p|,C|stop_gained|HIGH|OAT|4942|Transcript|NM_001171814.2|protein_coding|6/9||NM_001171814.2:c.483C>G|NP_001165285.1:p.Tyr161Ter|749/1811|483/906|161/301|Y/*|taC/taG|rs121965057&CM920525|1||-1|||EntrezGene||||||||likely_pathogenic&pathogenic||1&1|1737786&23076989&1609808&22674428|||||||-1|-3|-3|4|0.00|0.00|0.00|0.00|OAT|VUS|0.9785161|||AR|LP||||chr10:124402930-124402930|2.6295e-05|0|P|filter&vkgl&exit_p|,C|stop_gained|HIGH|OAT|4942|Transcript|NM_001322965.2|protein_coding|7/10||NM_001322965.2:c.897C>G|NP_001309894.1:p.Tyr299Ter|972/2034|897/1320|299/439|Y/*|taC/taG|rs121965057&CM920525|1||-1|||EntrezGene||||||||likely_pathogenic&pathogenic||1&1|1737786&23076989&1609808&22674428|||||||-1|-3|-3|4|0.00|0.00|0.00|0.00|OAT|VUS|0.98058724|||AR|LP||||chr10:124402930-124402930|2.6295e-05|0|P|filter&vkgl&exit_p|,C|stop_gained|HIGH|OAT|4942|Transcript|NM_001322966.2|protein_coding|8/11||NM_001322966.2:c.897C>G|NP_001309895.1:p.Tyr299Ter|1292/2354|897/1320|299/439|Y/*|taC/taG|rs121965057&CM920525|1||-1|||EntrezGene||||||||likely_pathogenic&pathogenic||1&1|1737786&23076989&1609808&22674428|||||||-1|-3|-3|4|0.00|0.00|0.00|0.00|OAT|VUS|0.9811948|||AR|LP||||chr10:124402930-124402930|2.6295e-05|0|P|filter&vkgl&exit_p|,C|stop_gained|HIGH|OAT|4942|Transcript|NM_001322967.2|protein_coding|8/11||NM_001322967.2:c.897C>G|NP_001309896.1:p.Tyr299Ter|1097/2159|897/1320|299/439|Y/*|taC/taG|rs121965057&CM920525|1||-1|||EntrezGene||||||||likely_pathogenic&pathogenic||1&1|1737786&23076989&1609808&22674428|||||||-1|-3|-3|4|0.00|0.00|0.00|0.00|OAT|VUS|0.9812247|||AR|LP||||chr10:124402930-124402930|2.6295e-05|0|P|filter&vkgl&exit_p|,C|stop_gained|HIGH|OAT|4942|Transcript|NM_001322968.2|protein_coding|9/12||NM_001322968.2:c.897C>G|NP_001309897.1:p.Tyr299Ter|1184/2246|897/1320|299/439|Y/*|taC/taG|rs121965057&CM920525|1||-1|||EntrezGene||||||||likely_pathogenic&pathogenic||1&1|1737786&23076989&1609808&22674428|||||||-1|-3|-3|4|0.00|0.00|0.00|0.00|OAT|VUS|0.9810348|||AR|LP||||chr10:124402930-124402930|2.6295e-05|0|P|filter&vkgl&exit_p|,C|stop_gained|HIGH|OAT|4942|Transcript|NM_001322969.2|protein_coding|8/11||NM_001322969.2:c.897C>G|NP_001309898.1:p.Tyr299Ter|1064/2126|897/1320|299/439|Y/*|taC/taG|rs121965057&CM920525|1||-1|||EntrezGene||||||||likely_pathogenic&pathogenic||1&1|1737786&23076989&1609808&22674428|||||||-1|-3|-3|4|0.00|0.00|0.00|0.00|OAT|VUS|0.98210436|||AR|LP||||chr10:124402930-124402930|2.6295e-05|0|P|filter&vkgl&exit_p|,C|stop_gained|HIGH|OAT|4942|Transcript|NM_001322970.2|protein_coding|9/12||NM_001322970.2:c.897C>G|NP_001309899.1:p.Tyr299Ter|1280/2342|897/1320|299/439|Y/*|taC/taG|rs121965057&CM920525|1||-1|||EntrezGene||||||||likely_pathogenic&pathogenic||1&1|1737786&23076989&1609808&22674428|||||||-1|-3|-3|4|0.00|0.00|0.00|0.00|OAT|VUS|0.9811948|||AR|LP||||chr10:124402930-124402930|2.6295e-05|0|P|filter&vkgl&exit_p|,C|stop_gained|HIGH|OAT|4942|Transcript|NM_001322971.2|protein_coding|5/8||NM_001322971.2:c.576C>G|NP_001309900.1:p.Tyr192Ter|656/1718|576/999|192/332|Y/*|taC/taG|rs121965057&CM920525|1||-1|||EntrezGene||||||||likely_pathogenic&pathogenic||1&1|1737786&23076989&1609808&22674428|||||||-1|-3|-3|4|0.00|0.00|0.00|0.00|OAT|VUS|0.9727213|||AR|LP||||chr10:124402930-124402930|2.6295e-05|0|P|filter&vkgl&exit_p|,C|stop_gained|HIGH|OAT|4942|Transcript|NM_001322974.2|protein_coding|7/10||NM_001322974.2:c.297C>G|NP_001309903.1:p.Tyr99Ter|863/1925|297/720|99/239|Y/*|taC/taG|rs121965057&CM920525|1||-1|||EntrezGene||||||||likely_pathogenic&pathogenic||1&1|1737786&23076989&1609808&22674428|||||||-1|-3|-3|4|0.00|0.00|0.00|0.00|OAT|VUS|0.974531|||AR|LP||||chr10:124402930-124402930|2.6295e-05|0|P|filter&vkgl&exit_p|	GT:VIPC_S	1/1:U1
-chr11	134144330	breakend2	G	G[8:61765143[	.	PASS	BND_DEPTH=39;CSQ=BND|intron_variant|MODIFIER|JAM3|83700|Transcript|NM_001205329.2|protein_coding||3/7|||||||||1||1|||EntrezGene|||||||||||||||||||||||||||||||||||||||P|filter&vkgl&clinVar&gnomad&effect&spliceAI&annotSV&impact&exit_p|,BND|coding_sequence_variant|MODIFIER|JAM3|83700|Transcript|NM_032801.5|protein_coding|4/9||||359/3765|347/933|116/310||||1||1||1|EntrezGene|||||||||||||||||||||||||||||||||||||||P|filter&vkgl&clinVar&gnomad&effect&spliceAI&annotSV&impact&exit_p|;MATEID=breakend1;MATE_BND_DEPTH=26;SVTYPE=BND	GT:VIPC_S	1/0:U1
 chr13	76995993	.	G	A	.	PASS	CSQ=A|missense_variant|MODERATE|CLN5|1203|Transcript|NM_001366624.2|protein_coding|3/5||NM_001366624.2:c.431G>A|NP_001353553.1:p.Cys144Tyr|449/5286|431/594|144/197|C/Y|tGt/tAt|rs1566219136|1||1|||EntrezGene|||||0|0.995||pathogenic||1||||||||-27|-43|-27|-1|0.00|0.00|0.01|0.00|CLN5|VUS|0.82795596|||AR|LP|||||||P|filter&vkgl&exit_p|,A|missense_variant|MODERATE|CLN5|1203|Transcript|NM_006493.4|protein_coding|3/4||NM_006493.4:c.431G>A|NP_006484.2:p.Cys144Tyr|449/5243|431/1077|144/358|C/Y|tGt/tAt|rs1566219136|1||1||1|EntrezGene|||||0|0.999||pathogenic||1||||||||-27|-43|-27|-1|0.00|0.00|0.01|0.00|CLN5|VUS|0.8734921|||AR|LP|||||||P|filter&vkgl&exit_p|	GT:VIPC_S	1/1:U1
 chr14	88870063	.	TG	T	.	PASS	CSQ=-|frameshift_variant|HIGH|TTC8|123016|Transcript|NM_001288781.1|protein_coding|12/16||NM_001288781.1:c.963del|NP_001275710.1:p.Met321IlefsTer15|1159/2378|963/1596|321/531|M/X|atG/at|rs1431207606|1||1|||EntrezGene||||||||likely_pathogenic||1||||||||18|-4|-9|-4|0.00|0.16|0.00|0.00|TTC8|VUS|0.9879852|HP:0000951||AR|LP|||||||P|filter&vkgl&exit_p|,-|frameshift_variant|HIGH|TTC8|123016|Transcript|NM_001288782.1|protein_coding|10/14||NM_001288782.1:c.321del|NP_001275711.1:p.Met107IlefsTer15|1079/2298|321/954|107/317|M/X|atG/at|rs1431207606|1||1|||EntrezGene||||||||likely_pathogenic||1||||||||18|-4|-9|-4|0.00|0.16|0.00|0.00|TTC8|VUS|0.985551|HP:0000951||AR|LP|||||||P|filter&vkgl&exit_p|,-|frameshift_variant|HIGH|TTC8|123016|Transcript|NM_001288783.1|protein_coding|11/15||NM_001288783.1:c.198del|NP_001275712.1:p.Met66IlefsTer15|1051/2270|198/831|66/276|M/X|atG/at|rs1431207606|1||1|||EntrezGene||||||||likely_pathogenic||1||||||||18|-4|-9|-4|0.00|0.16|0.00|0.00|TTC8|VUS|0.98350626|HP:0000951||AR|LP|||||||P|filter&vkgl&exit_p|,-|frameshift_variant|HIGH|TTC8|123016|Transcript|NM_001366535.2|protein_coding|10/13||NM_001366535.2:c.885del|NP_001353464.1:p.Met295IlefsTer15|942/5160|885/1434|295/477|M/X|atG/at|rs1431207606|1||1|||EntrezGene||||||||likely_pathogenic||1||||||||18|-4|-9|-4|0.00|0.16|0.00|0.00|TTC8|VUS|0.9825065|HP:0000951||AR|LP|||||||P|filter&vkgl&exit_p|,-|frameshift_variant|HIGH|TTC8|123016|Transcript|NM_001366536.2|protein_coding|9/12||NM_001366536.2:c.795del|NP_001353465.1:p.Met265IlefsTer15|852/5070|795/1344|265/447|M/X|atG/at|rs1431207606|1||1|||EntrezGene||||||||likely_pathogenic||1||||||||18|-4|-9|-4|0.00|0.16|0.00|0.00|TTC8|VUS|0.9880476|HP:0000951||AR|LP|||||||P|filter&vkgl&exit_p|,-|frameshift_variant|HIGH|TTC8|123016|Transcript|NM_144596.4|protein_coding|11/15||NM_144596.4:c.915del|NP_653197.2:p.Met305IlefsTer15|972/2183|915/1548|305/515|M/X|atG/at|rs1431207606|1||1||1|EntrezGene||||||||likely_pathogenic||1||||||||18|-4|-9|-4|0.00|0.16|0.00|0.00|TTC8|VUS|0.97812086|HP:0000951||AR|LP|||||||P|filter&vkgl&exit_p|,-|frameshift_variant|HIGH|TTC8|123016|Transcript|NM_198309.3|protein_coding|11/15||NM_198309.3:c.885del|NP_938051.1:p.Met295IlefsTer15|1081/2300|885/1518|295/505|M/X|atG/at|rs1431207606|1||1|||EntrezGene||||||||likely_pathogenic||1||||||||18|-4|-9|-4|0.00|0.16|0.00|0.00|TTC8|VUS|0.9879701|HP:0000951||AR|LP|||||||P|filter&vkgl&exit_p|,-|frameshift_variant|HIGH|TTC8|123016|Transcript|NM_198310.3|protein_coding|10/14||NM_198310.3:c.795del|NP_938052.1:p.Met265IlefsTer15|991/2210|795/1428|265/475|M/X|atG/at|rs1431207606|1||1|||EntrezGene||||||||likely_pathogenic||1||||||||18|-4|-9|-4|0.00|0.16|0.00|0.00|TTC8|VUS|0.98293847|HP:0000951||AR|LP|||||||P|filter&vkgl&exit_p|,-|non_coding_transcript_exon_variant|MODIFIER|TTC8|123016|Transcript|NR_159362.2|misc_RNA|11/15||NR_159362.2:n.1002del||1002/5304|||||rs1431207606|1||1|||EntrezGene||||||||likely_pathogenic||1||||||||18|-4|-9|-4|0.00|0.16|0.00|0.00|TTC8|VUS|0.20394427|HP:0000951||AR|LP|||||||P|filter&vkgl&exit_p|	GT:VIPC_S	0|1:U1
 chr14	104701523	.	T	G	.	PASS	CSQ=G|missense_variant|MODERATE|INF2|64423|Transcript|NM_001031714.4|protein_coding|2/22||NM_001031714.4:c.158T>G|NP_001026884.3:p.Leu53Arg|289/7566|158/3723|53/1240|L/R|cTg/cGg||1||1|||EntrezGene|||||0|0.999||||||||||||-28|-2|37|-2|0.00|0.00|0.00|0.00|INF2|VUS|0.89743406|||AD|LP|||||||P|filter&vkgl&exit_p|,G|missense_variant|MODERATE|INF2|64423|Transcript|NM_022489.4|protein_coding|2/23||NM_022489.4:c.158T>G|NP_071934.3:p.Leu53Arg|289/7623|158/3750|53/1249|L/R|cTg/cGg||1||1||1|EntrezGene|||||0|0.999||||||||||||-28|-2|37|-2|0.00|0.00|0.00|0.00|INF2|VUS|0.89743406|||AD|LP|||||||P|filter&vkgl&exit_p|,G|missense_variant|MODERATE|INF2|64423|Transcript|NM_032714.3|protein_coding|2/5||NM_032714.3:c.158T>G|NP_116103.1:p.Leu53Arg|289/1692|158/705|53/234|L/R|cTg/cGg||1||1|||EntrezGene|||||0|0.999||||||||||||-28|-2|37|-2|0.00|0.00|0.00|0.00|INF2|VUS|0.89743406|||AD|LP|||||||P|filter&vkgl&exit_p|	GT:VIPC_S	0/0:U1

package/src/utils/query/query.ts

@@ -18,7 +18,7 @@ export function createQuery(
   const queryParts: Query[] = [];
 
   const queryVariantType = createQueryVariantType(variantType);
-  if (queryVariantType !== null) {
+  if (queryVariantType !== null && Object.hasOwn(meta.records.info, "SVTYPE")) {
     queryParts.push(queryVariantType);
   }
 

package/tests/utils/query/query.test.ts

@@ -37,6 +37,7 @@ describe("query", () => {
       const fieldMetadata = { id: "GT", number: { type: "NUMBER", count: 1 } } as FieldMetadataWrapper;
       const vcfMetadata = {
         format: { GT: fieldMetadata },
+        info: { SVTYPE: fieldMetadata},
       } as Partial<VcfMetadataContainer> as VcfMetadataContainer;
       const meta = {
         app: {},
@@ -60,6 +61,33 @@ describe("query", () => {
       expect(createQueryFilters).toHaveBeenCalledWith(configFilters, filterValues);
     });
 
+    test("variant type missing, sample and filters", () => {
+      const querySample: Query = { selector: "c", operator: "==", args: "d" };
+      const queryFilters: Query = { selector: "e", operator: "==", args: "f" };
+      const fieldMetadata = { id: "GT", number: { type: "NUMBER", count: 1 } } as FieldMetadataWrapper;
+      const vcfMetadata = {
+        format: { GT: fieldMetadata },
+        info: {  },
+      } as Partial<VcfMetadataContainer> as VcfMetadataContainer;
+      const meta = {
+        app: {},
+        records: vcfMetadata,
+        variantTypeIds: {},
+      } as MetadataContainer;
+      vi.mocked(createQuerySample).mockReturnValue(querySample);
+      vi.mocked(createQueryFilters).mockReturnValue(queryFilters);
+
+      expect(createQuery(config, meta, variantType, sample, filterValues)).toStrictEqual({
+        args: [
+          { selector: "c", operator: "==", args: "d" },
+          { selector: "e", operator: "==", args: "f" },
+        ],
+        operator: "and",
+      });
+      expect(createQuerySample).toHaveBeenCalledWith(configVip, sample, meta);
+      expect(createQueryFilters).toHaveBeenCalledWith(configFilters, filterValues);
+    });
+
     test("sample", () => {
       const querySample: Query = { selector: "c", operator: "==", args: "d" };
       const fieldMetadata = { id: "GT", number: { type: "NUMBER", count: 1 } } as FieldMetadataWrapper;