@molgenis/vip-report-template 6.1.1 → 7.0.0

package/src/components/record/Info.tsx

@@ -1,55 +0,0 @@
-import { Component, Match, Switch } from "solid-js";
-import { FieldMetadata } from "@molgenis/vip-report-vcf/src/MetadataParser";
-import { Consequence } from "./info/Consequence";
-import { Field, FieldContext, FieldValue } from "./field/Field";
-import { Gene } from "./info/Gene";
-import { PubMed } from "./info/PubMed";
-import { Hgvs } from "./info/Hgvs";
-import { ClinVar } from "./info/ClinVar";
-import { GnomAD } from "./info/GnomAD";
-import { isAnyCsqInfo, isCsqInfo } from "../../utils/csqUtils";
-import { Vkgl } from "./info/Vkgl";
-import { InheritanceModes } from "./info/InheritanceModes";
-import { Hpo } from "./info/Hpo";
-import { VipC } from "./info/VipC";
-
-export const Info: Component<{
-  info: FieldValue;
-  infoMeta: FieldMetadata;
-  context: FieldContext;
-}> = (props) => {
-  return (
-    <Switch fallback={<Field {...props} />}>
-      <Match when={isCsqInfo(props.infoMeta, "Consequence")}>
-        <Consequence {...props} />
-      </Match>
-      <Match when={isCsqInfo(props.infoMeta, "PUBMED")}>
-        <PubMed {...props} />
-      </Match>
-      <Match when={isCsqInfo(props.infoMeta, "SYMBOL")}>
-        <Gene {...props} />
-      </Match>
-      <Match when={isCsqInfo(props.infoMeta, "InheritanceModesGene")}>
-        <InheritanceModes {...props} />
-      </Match>
-      <Match when={isCsqInfo(props.infoMeta, "gnomAD_AF")}>
-        <GnomAD {...props} />
-      </Match>
-      <Match when={isAnyCsqInfo(props.infoMeta, ["HGVSc", "HGVSp"])}>
-        <Hgvs {...props} />
-      </Match>
-      <Match when={isCsqInfo(props.infoMeta, "clinVar_CLNSIG")}>
-        <ClinVar {...props} />
-      </Match>
-      <Match when={isCsqInfo(props.infoMeta, "VKGL_CL")}>
-        <Vkgl {...props} />
-      </Match>
-      <Match when={isCsqInfo(props.infoMeta, "HPO")}>
-        <Hpo {...props} />
-      </Match>
-      <Match when={isCsqInfo(props.infoMeta, "VIPC")}>
-        <VipC {...props} />
-      </Match>
-    </Switch>
-  );
-};

package/src/components/record/Pos.tsx

@@ -1,5 +0,0 @@
-import { Component } from "solid-js";
-
-export const Pos: Component<{ value: number }> = (props) => {
-  return <span>{props.value}</span>;
-};

package/src/components/record/Qual.tsx

@@ -1,5 +0,0 @@
-import { Component } from "solid-js";
-
-export const Qual: Component<{ value: number | null }> = (props) => {
-  return <>{props.value && <span>{props.value}</span>}</>;
-};

package/src/components/record/RecordDownload.tsx

@@ -1,66 +0,0 @@
-import { Component } from "solid-js";
-import { HtsFileMetadata, Query, Sample } from "@molgenis/vip-report-api/src/Api";
-import { Metadata } from "@molgenis/vip-report-vcf/src/Vcf";
-import api from "../../Api";
-import { Filter, writeVcf } from "@molgenis/vip-report-vcf/src/VcfWriter";
-
-export const RecordDownload: Component<{ recordsMetadata: Metadata; query?: Query; samples?: Sample[] }> = (props) => {
-  const filter = (): Filter | undefined =>
-    props.samples ? { samples: props.samples.map((sample) => sample.person.individualId) } : undefined;
-
-  function parseFilename(htsFile: HtsFileMetadata) {
-    return htsFile.uri.split("\\").pop()?.split("/").pop()?.split(".").shift();
-  }
-
-  // derived from https://stackoverflow.com/a/19176102
-  function getDateTimeString() {
-    const now = new Date();
-
-    const year = now.getFullYear().toString();
-    let month = (now.getMonth() + 1).toString();
-    let day = now.getDate().toString();
-    let hour = now.getHours().toString();
-    let minute = now.getMinutes().toString();
-    let second = now.getSeconds().toString();
-
-    if (month.length == 1) month = "0" + month;
-    if (day.length == 1) day = "0" + day;
-    if (hour.length == 1) hour = "0" + hour;
-    if (minute.length == 1) minute = "0" + minute;
-    if (second.length == 1) second = "0" + second;
-
-    return year + month + day + "_" + hour + minute + second;
-  }
-
-  function onClick() {
-    const handler = async () => {
-      const records = await api.getRecords({ query: props.query, size: Number.MAX_SAFE_INTEGER });
-      const vcf = writeVcf({ metadata: props.recordsMetadata, data: records.items.map((item) => item.data) }, filter());
-
-      const url = window.URL.createObjectURL(new Blob([vcf]));
-      const link = document.createElement("a");
-      link.href = url;
-      const htsFile = await api.getHtsFileMetadata();
-      const filename = parseFilename(htsFile) as string;
-      link.setAttribute("download", filename + "_report_" + getDateTimeString() + ".vcf");
-      document.body.appendChild(link);
-      link.click();
-      document.body.removeChild(link);
-    };
-    handler().catch((error) => console.error(error));
-  }
-
-  return (
-    <div class="control">
-      <button
-        class="button is-info"
-        onClick={onClick}
-        title="Download vcf file with records matching filters and search queries"
-      >
-        <span class="icon is-small">
-          <i class="fas fa-download" />
-        </span>
-      </button>
-    </div>
-  );
-};

package/src/components/record/Ref.tsx

@@ -1,6 +0,0 @@
-import { Component } from "solid-js";
-import { Allele } from "./Allele";
-
-export const Ref: Component<{ value: string; isAbbreviate: boolean }> = (props) => {
-  return <Allele value={props.value} isAbbreviate={props.isAbbreviate} />;
-};

package/src/components/record/field/Field.tsx

@@ -1,36 +0,0 @@
-import { Component } from "solid-js";
-import { Value } from "@molgenis/vip-report-vcf/src/ValueParser";
-import { FieldMetadata } from "@molgenis/vip-report-vcf/src/MetadataParser";
-import { FieldSingleValue } from "./FieldSingleValue";
-import { FieldMultipleValue } from "./FieldMultipleValue";
-import { Record } from "@molgenis/vip-report-vcf/src/Vcf";
-import { Item } from "@molgenis/vip-report-api/src/Api";
-
-export type FieldProps = {
-  info: FieldValue;
-  infoMeta: FieldMetadata;
-  context: FieldContext;
-};
-
-export type FieldValue = {
-  value: Value | Value[];
-  valueParent?: Value | Value[];
-  record: Item<Record>;
-};
-
-export type FieldContext = {
-  genomeAssembly?: string;
-  isPossibleCompound?: boolean;
-};
-
-export const Field: Component<FieldProps> = (props) => {
-  return (
-    <>
-      {props.infoMeta.number.count === 1 ? (
-        <FieldSingleValue info={props.info.value as Value} infoMetadata={props.infoMeta} />
-      ) : (
-        <FieldMultipleValue info={props.info.value as Value[]} infoMetadata={props.infoMeta} />
-      )}
-    </>
-  );
-};

package/src/components/record/field/FieldMultipleValue.tsx

@@ -1,22 +0,0 @@
-import { Component, For } from "solid-js";
-import { Value } from "@molgenis/vip-report-vcf/src/ValueParser";
-import { FieldMetadata } from "@molgenis/vip-report-vcf/src/MetadataParser";
-import { FieldSingleValue } from "./FieldSingleValue";
-
-export const FieldMultipleValue: Component<{
-  info: Value[];
-  infoMetadata: FieldMetadata;
-}> = (props) => {
-  return (
-    <>
-      <For each={props.info}>
-        {(value, i) => (
-          <>
-            {i() !== 0 && <span>, </span>}
-            <FieldSingleValue info={value} infoMetadata={props.infoMetadata} />
-          </>
-        )}
-      </For>
-    </>
-  );
-};

package/src/components/record/field/FieldSingleValue.tsx

@@ -1,35 +0,0 @@
-import { Component, Match, Switch } from "solid-js";
-import { Value } from "@molgenis/vip-report-vcf/src/ValueParser";
-import { FieldMetadata } from "@molgenis/vip-report-vcf/src/MetadataParser";
-import { FieldValueFloat } from "./FieldValueFloat";
-import { FieldValueString } from "./FieldValueString";
-import { FieldValueCharacter } from "./FieldValueCharacter";
-import { FieldValueInteger } from "./FieldValueInteger";
-import { FieldValueFlag } from "./FieldValueFlag";
-import { Error } from "../../Error";
-
-export const FieldSingleValue: Component<{
-  info: Value;
-  infoMetadata: FieldMetadata;
-}> = (props) => {
-  const type = () => props.infoMetadata.type;
-  return (
-    <Switch fallback={<Error error={`invalid info type ${type()}`} />}>
-      <Match when={type() === "CATEGORICAL" || type() === "STRING"}>
-        <FieldValueString value={props.info as string} />
-      </Match>
-      <Match when={type() === "CHARACTER"}>
-        <FieldValueCharacter value={props.info as string} />
-      </Match>
-      <Match when={type() === "FLAG"}>
-        <FieldValueFlag value={props.info as boolean} />
-      </Match>
-      <Match when={type() === "FLOAT"}>
-        <FieldValueFloat value={props.info as number} />
-      </Match>
-      <Match when={type() === "INTEGER"}>
-        <FieldValueInteger value={props.info as number} />
-      </Match>
-    </Switch>
-  );
-};

package/src/components/record/info/ClinVar.tsx

@@ -1,81 +0,0 @@
-import { Component, Show } from "solid-js";
-import { FieldProps } from "../field/Field";
-import { Anchor } from "../../Anchor";
-import { Abbr } from "../../Abbr";
-import { getCsqInfo, getCsqInfoIndex } from "../../../utils/csqUtils";
-
-export const ClinVar: Component<FieldProps> = (props) => {
-  const label = () => {
-    const classes = props.info.value as string[] | null;
-    return classes
-      ? classes
-          .map((token) => {
-            switch (token.toLowerCase()) {
-              case "benign":
-                return "B";
-              case "likely_benign":
-                return "LB";
-              case "uncertain_significance":
-                return "VUS";
-              case "likely_pathogenic":
-                return "LP";
-              case "pathogenic":
-                return "P";
-              case "conflicting_interpretations_of_pathogenicity":
-                return "Conflict";
-              default:
-                return token;
-            }
-          })
-          .join(", ")
-      : null;
-  };
-
-  const href = () => {
-    const clinVarIdsField = getCsqInfoIndex(props.infoMeta, "clinVar_CLNID");
-    const clinVarIds = clinVarIdsField !== -1 ? (getCsqInfo(props.info, clinVarIdsField) as number[]) : [];
-    return clinVarIds.length === 1 ? `https://www.ncbi.nlm.nih.gov/clinvar/variation/${clinVarIds[0]}/` : undefined;
-  };
-
-  const description = () => {
-    const statusField = getCsqInfoIndex(props.infoMeta, "clinVar_CLNREVSTAT");
-    const status = statusField !== -1 ? (getCsqInfo(props.info, statusField) as string[]) : [];
-    if (status.length === 0) return;
-
-    let description;
-    if (status.length === 1 && status.includes("practice_guideline")) {
-      description = "\u2605\u2605\u2605\u2605";
-    } else if (status.length === 1 && status.includes("reviewed_by_expert_panel")) {
-      description = "\u2605\u2605\u2605\u2606";
-    } else if (
-      status.length === 3 &&
-      status.includes("criteria_provided") &&
-      status.includes("_multiple_submitters") &&
-      status.includes("_no_conflicts")
-    ) {
-      description = "\u2605\u2605\u2606\u2606";
-    } else if (
-      status.length === 2 &&
-      status.includes("criteria_provided") &&
-      status.includes("_conflicting_interpretations")
-    ) {
-      description = "\u2605\u2606\u2606\u2606";
-    } else if (status.length === 2 && status.includes("criteria_provided") && status.includes("_single_submitter")) {
-      description = "\u2605\u2606\u2606\u2606";
-    } else {
-      description = "\u2606\u2606\u2606\u2606";
-    }
-    description += " (" + status.map((status) => status.replaceAll("_", " ").trim()).join(", ") + ")";
-    return description;
-  };
-
-  return (
-    <Show when={label()} keyed>
-      {(label) => (
-        <Anchor href={href()}>
-          {description() ? <Abbr title={description()!} value={label} /> : <span>{label}</span>}
-        </Anchor>
-      )}
-    </Show>
-  );
-};

package/src/components/record/info/Consequence.tsx

@@ -1,18 +0,0 @@
-import { Component } from "solid-js";
-import { FieldProps } from "../field/Field";
-import { Abbr } from "../../Abbr";
-
-export const Consequence: Component<FieldProps> = (props) => {
-  const consequence = (): string[] => props.info.value as string[];
-
-  return (
-    <>
-      <span>{consequence()[0]}</span>
-      {consequence().length > 1 && (
-        <span>
-          , <Abbr title={consequence().slice(1).join(", ")} value={"\u2026"} />
-        </span>
-      )}
-    </>
-  );
-};

package/src/components/record/info/Gene.tsx

@@ -1,56 +0,0 @@
-import { Component, createMemo, Show } from "solid-js";
-import { Anchor } from "../../Anchor";
-import { FieldProps } from "../field/Field";
-import { ValueFlag, ValueString } from "@molgenis/vip-report-vcf/src/ValueParser";
-import { getCsqInfo, getCsqInfoIndex } from "../../../utils/csqUtils";
-import { Abbr } from "../../Abbr";
-
-export const Gene: Component<FieldProps> = (props) => {
-  const symbol = (): ValueString => props.info.value as ValueString;
-
-  const symbolSource = createMemo((): ValueString | undefined => {
-    if (symbol() === null) return undefined;
-
-    const symbolSourceFieldIndex = getCsqInfoIndex(props.infoMeta, "SYMBOL_SOURCE");
-    return symbolSourceFieldIndex !== -1 ? (getCsqInfo(props.info, symbolSourceFieldIndex) as ValueString) : undefined;
-  });
-
-  const geneId = createMemo((): ValueString | undefined => {
-    if (symbol() === null) return undefined;
-
-    const geneFieldIndex = getCsqInfoIndex(props.infoMeta, "Gene");
-    return geneFieldIndex !== -1 ? (getCsqInfo(props.info, geneFieldIndex) as ValueString) : undefined;
-  });
-
-  const href = (): string | undefined => {
-    if (symbol() === null) return undefined;
-
-    const queryString =
-      symbolSource() === "EntrezGene" && geneId()
-        ? `query=ncbi_gene_id:${geneId()!}`
-        : `query=${encodeURIComponent(symbol()!)}&filter=document_type:%22gene%22`;
-    return `https://www.genenames.org/tools/search/#!/?${queryString}`;
-  };
-
-  const incompletePenetrance = (): ValueFlag | undefined => {
-    const ipFieldIndex = getCsqInfoIndex(props.infoMeta, "IncompletePenetrance");
-    return ipFieldIndex !== -1 ? (getCsqInfo(props.info, ipFieldIndex) as ValueFlag) : undefined;
-  };
-
-  return (
-    <Show when={symbol()} keyed>
-      {(symbol) => (
-        <>
-          <Anchor href={href()}>
-            <span>{symbol}</span>
-          </Anchor>
-          {incompletePenetrance() && (
-            <span class="ml-1">
-              <Abbr title="gene is known for incomplete penetrance" value="IP" />
-            </span>
-          )}
-        </>
-      )}
-    </Show>
-  );
-};

package/src/components/record/info/GnomAD.tsx

@@ -1,54 +0,0 @@
-import { Component, Show } from "solid-js";
-import { FieldValueFloat } from "../field/FieldValueFloat";
-import { FieldProps } from "../field/Field";
-import { ValueFloat } from "@molgenis/vip-report-vcf/src/ValueParser";
-import { Anchor } from "../../Anchor";
-import { getCsqInfo, getCsqInfoIndex } from "../../../utils/csqUtils";
-
-export const GnomAD: Component<FieldProps> = (props) => {
-  const af = (): number | null => props.info.value as ValueFloat;
-
-  const qcIndex = (): number => getCsqInfoIndex(props.infoMeta, "gnomAD_QC");
-  const qc = (): string[] => (qcIndex() !== -1 ? (getCsqInfo(props.info, qcIndex()) as string[]) : []);
-  const covIndex = (): number => getCsqInfoIndex(props.infoMeta, "gnomAD_COV");
-  const cov = (): number | null => (covIndex() !== -1 ? (getCsqInfo(props.info, covIndex()) as number) : null);
-
-  const href = (): string | undefined => {
-    let href;
-    if (af() !== null) {
-      const record = props.info.record.data;
-      // FIXME record.a incorrect: select record.a through CSQ:ALLELE_NUM
-      const variantId = [record.c, record.p, record.r, record.a].join("-");
-      const dataset = "gnomad_r4";
-      href = `https://gnomad.broadinstitute.org/variant/${encodeURIComponent(variantId)}?dataset=${dataset}`;
-    }
-    return href;
-  };
-
-  return (
-    <Show when={af() !== null}>
-      <Show when={href()} fallback={<FieldValueFloat value={af()} />} keyed>
-        {(href) => (
-          <>
-            <Anchor href={href}>
-              <FieldValueFloat value={af()} />
-            </Anchor>
-            <Show when={qc().length > 0}>
-              <abbr title={"Failed quality control filters: " + qc().join(", ")} class="ml-1 is-clickable">
-                <i class="fas fa-circle-exclamation has-text-warning" />
-              </abbr>
-            </Show>
-            <Show when={cov() != null && cov() < 0.5}>
-              <abbr
-                title="This variant is covered in fewer than 50% of individuals in gnomAD. This may indicate a low-quality site."
-                class="ml-1 is-clickable"
-              >
-                <i class="fas fa-circle-exclamation has-text-warning" />
-              </abbr>
-            </Show>
-          </>
-        )}
-      </Show>
-    </Show>
-  );
-};

package/src/components/record/info/Hpo.tsx

@@ -1,52 +0,0 @@
-import { Component, For, Show } from "solid-js";
-import { Anchor } from "../../Anchor";
-import { FieldProps } from "../field/Field";
-import { getCsqInfo, getCsqInfoIndex } from "../../../utils/csqUtils";
-import { FieldValueString } from "../field/FieldValueString";
-
-type HpoTerm = {
-  id: string;
-  href: string;
-};
-
-export const Hpo: Component<FieldProps> = (props) => {
-  const hpoTerms = (): HpoTerm[] =>
-    (props.info.value as string[]).map((hpoTermId) => ({
-      id: hpoTermId,
-      href: `https://hpo.jax.org/app/browse/term/${encodeURI(hpoTermId)}`,
-    }));
-
-  const gadoIndex = (): number => getCsqInfoIndex(props.infoMeta, "GADO_PD");
-  const gadoClass = (): string | null => (gadoIndex() !== -1 ? (getCsqInfo(props.info, gadoIndex()) as string) : null);
-
-  return (
-    <>
-      <For each={hpoTerms()}>
-        {(hpoTerm, i) => (
-          <>
-            {i() !== 0 && <span>, </span>}
-            <Anchor href={hpoTerm.href}>
-              <FieldValueString value={hpoTerm.id} />
-            </Anchor>
-          </>
-        )}
-      </For>
-      <Show when={gadoClass() !== null && gadoClass() === "LC"} keyed>
-        <abbr
-          title="Gene phenotype relation predicted by GADO with low confidence; Z-Score greater than 3 but below 5."
-          class="ml-1 is-clickable"
-        >
-          <i class="fas fa-question-circle has-text-info" />
-        </abbr>
-      </Show>
-      <Show when={gadoClass() !== null && gadoClass() === "HC"} keyed>
-        <abbr
-          title="Gene phenotype relation predicted by GADO with high confidence; Z-Score greater than 5."
-          class="ml-1 is-clickable"
-        >
-          <i class="fas fa-info-circle has-text-info" />
-        </abbr>
-      </Show>
-    </>
-  );
-};

package/src/components/record/info/InheritanceModes.tsx

@@ -1,22 +0,0 @@
-import { Component, Show } from "solid-js";
-import { Value, ValueString } from "@molgenis/vip-report-vcf/src/ValueParser";
-import { FieldProps } from "../field/Field";
-import { FieldMultipleValue } from "../field/FieldMultipleValue";
-
-export const InheritanceModes: Component<FieldProps> = (props) => {
-  const inheritanceModesGene: ValueString[] = props.info.value as ValueString[];
-  let isArInheritance = false;
-  if (inheritanceModesGene.includes("AR") || inheritanceModesGene.length === 0) {
-    isArInheritance = props.context.isPossibleCompound !== undefined && props.context.isPossibleCompound;
-  }
-  return (
-    <>
-      <FieldMultipleValue info={props.info.value as Value[]} infoMetadata={props.infoMeta} />
-      <Show when={isArInheritance} keyed>
-        <abbr title="Variant is possibly part of a compound." class="ml-1 is-clickable">
-          <i class="fas fa-circle-exclamation has-text-info" />
-        </abbr>
-      </Show>
-    </>
-  );
-};

package/src/components/record/info/VipC.tsx

@@ -1,23 +0,0 @@
-import { Component, Show } from "solid-js";
-import { Abbr } from "../../Abbr";
-import { FieldProps } from "../field/Field";
-import { ValueString } from "@molgenis/vip-report-vcf/src/ValueParser";
-import { getCsqInfo, getCsqInfoIndex } from "../../../utils/csqUtils";
-
-export const VipC: Component<FieldProps> = (props) => {
-  const value = () => props.info.value as ValueString;
-  const description = () => {
-    const fieldIndex = getCsqInfoIndex(props.infoMeta, "VIPP");
-    return fieldIndex !== -1 ? (getCsqInfo(props.info, fieldIndex) as ValueString[]) : null;
-  };
-
-  return (
-    <Show when={value()} keyed>
-      {(value) => (
-        <Show when={description()} fallback={value} keyed>
-          {(description) => <Abbr title={description.join(", ")} value={value} />}
-        </Show>
-      )}
-    </Show>
-  );
-};

package/src/components/record/info/Vkgl.tsx

@@ -1,42 +0,0 @@
-import { Component, Show } from "solid-js";
-import { Abbr } from "../../Abbr";
-import { FieldProps } from "../field/Field";
-import { ValueString } from "@molgenis/vip-report-vcf/src/ValueParser";
-import { getCsqInfo, getCsqInfoIndex } from "../../../utils/csqUtils";
-
-export const Vkgl: Component<FieldProps> = (props) => {
-  const value = () => props.info.value as ValueString;
-  const title = () => {
-    if (value() === null) return undefined;
-
-    const labs: { [key: string]: string } = {
-      VKGL_AMC: "AMC",
-      VKGL_ERASMUS: "Erasmus",
-      VKGL_LUMC: "LUMC",
-      VKGL_NKI: "NKI",
-      VKGL_RADBOUD_MUMC: "Radboud/MUMC",
-      VKGL_UMCG: "UMCG",
-      VKGL_UMCU: "UMCU",
-      VKGL_VUMC: "VUMC",
-    };
-
-    const descriptions = [];
-    for (const key in labs) {
-      const fieldIndex = getCsqInfoIndex(props.infoMeta, key);
-      if (fieldIndex !== -1) {
-        const value = getCsqInfo(props.info, fieldIndex) as ValueString;
-        if (value !== null) descriptions.push(`${labs[key]}:${value}`);
-      }
-    }
-    return descriptions.length > 0 ? descriptions.join(", ") : null;
-  };
-  return (
-    <Show when={value()} keyed>
-      {(value) => (
-        <Show when={title()} fallback={<span>{value}</span>} keyed>
-          {(title) => <Abbr title={title} value={value} />}
-        </Show>
-      )}
-    </Show>
-  );
-};

package/src/mocks/GRCh37/vcf/no_vep.vcf.blob

@@ -1,61 +0,0 @@
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-##fileDate=20200320
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-##contig=<ID=Y,length=59373566,assembly=b37>
-##contig=<ID=MT,length=16569,assembly=b37>
-##ALT=<ID=DEL,Description="Deletion">
-##ALT=<ID=INS,Description="Insertion">
-##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=MATEID,Number=.,Type=String,Description="ID of mate breakend">
-##INFO=<ID=BND_DEPTH,Number=1,Type=Integer,Description="Read depth at local translocation breakend">
-##INFO=<ID=MATE_BND_DEPTH,Number=1,Type=Integer,Description="Read depth at remote translocation mate breakend">
-##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
-##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read Depth">
-#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	Patient	Father	Mother	Sister	Nephew	Unrelated
-1	10042538	.	C	T	.	PASS	.	GT:DP	1|0:50	0|0:10	0|0:50	0|0:50	0|0:50	0|0:50
-1	152520788	symbolic1	A	<DEL>	.	PASS	SVLEN=-49314;SVTYPE=DEL	GT:DP	1|0:50	0|0:10	0|0:50	0|0:50	0|0:50	0|0:50
-2	47635667	symbolic2	G	<INS>	.	PASS	SVLEN=-49314;SVTYPE=INS	GT:DP	1|0:50	0|0:10	0|0:50	0|0:50	0|0:50	0|0:50
-4	106320294	.	G	A	.	PASS	.	GT:DP	1|0:50	0|0:10	0|0:50	0|0:50	0|0:50	0|0:50
-7	42017311	single_breakend_nation	C	C.	.	PASS	SVTYPE=BND	GT:DP	1|0:50	0|0:10	0|0:50	0|0:50	0|0:50	0|0:50
-7	42064957	.	GACTC	G	.	PASS	.	GT:DP	1|0:50	0|0:10	0|0:50	0|0:50	0|0:50	0|0:50
-8	61765143	breakend1	G	]11:134014225]G	.	PASS	SVTYPE=BND;MATEID=breakend2;BND_DEPTH=26;MATE_BND_DEPTH=39	GT:DP	1|0:50	0|0:10	0|0:50	0|0:50	0|0:50	0|0:50
-8	145140500	.	CAG	C	.	PASS	.	GT:DP	1|0:50	0|0:10	0|0:50	0|0:50	0|0:50	0|0:50
-9	107546633	.	AAAGAT	A	.	PASS	.	GT:DP	1|0:50	0|0:10	0|0:50	0|0:50	0|0:50	0|0:50
-10	126091499	.	G	C	.	PASS	.	GT:DP	1|0:50	0|0:10	0|0:50	0|0:50	0|0:50	0|0:50
-11	134014225	breakend2	G	G[8:61765143[	.	PASS	SVTYPE=BND;MATEID=breakend1;BND_DEPTH=39;MATE_BND_DEPTH=26	GT:DP	1|0:50	0|0:10	0|0:50	0|0:50	0|0:50	0|0:50
-13	77570128	.	G	A	.	PASS	.	GT:DP	1|0:50	0|0:10	0|0:50	0|0:50	0|0:50	0|0:50
-14	89336407	.	TG	T	.	PASS	.	GT:DP	1|0:50	0|0:10	0|0:50	0|0:50	0|0:50	0|0:50
-14	105167860	.	T	G	.	PASS	.	GT:DP	1|0:50	0|0:10	0|0:50	0|0:50	0|0:50	0|0:50
-17	29556064	.	AC	A	.	PASS	.	GT:DP	1|0:50	0|0:10	0|0:50	0|0:50	0|0:50	0|0:50
-17	29663879	.	T	G	.	PASS	.	GT:DP	1|0:50	0|0:10	0|0:50	0|0:50	0|0:50	0|0:50
-19	11216146	.	C	G	.	PASS	.	GT:DP	1|0:50	0|0:10	0|0:50	0|0:50	0|0:50	0|0:50
-19	17451997	.	GA	G	.	PASS	.	GT:DP	1|0:50	0|0:10	0|0:50	0|0:50	0|0:50	0|0:50
-20	62326992	.	C	T	.	PASS	.	GT:DP	1|0:50	0|0:10	0|0:50	0|0:50	0|0:50	0|0:50
-22	50627593	.	C	CTG	.	.	.	GT:DP	1|0:50	0|0:10	0|0:50	0|0:50	0|0:50	0|0:50
-22	50721546	.	C	T	.	PASS	.	GT:DP	1|0:50	0|0:10	0|0:50	0|0:50	0|0:50	0|0:50
-X	48933021	x_chrom	A	T	.	PASS	.	GT:DP	1|0:50	0|0:10	0|0:50	0|0:50	0|0:50	0|0:50
-Y	2655641	y_chrom	G	A	.	PASS	.	GT:DP	1:50	0:10	.	.	1:50	1:50
-MT	15326	mt_chrom	A	G	.	PASS	.	GT:DP	1|0:50	0|0:10	0|0:50	0|0:50	0|0:50	0|0:50