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GenomePaint VCF Track Example

Zhou Lab

Sep 28, 2021

5.2K

Whole Genome Sequencing

The VCF track features a population frequency filter, coverage-VAF plot, sample line plot, boxplot by genotype, and sophisticated methods for displaying metadata (see summary here). The current implement only accepts SNV/indel data. Learn more about the VCF track.

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runproteinpaint({
  host: "https://proteinpaint.stjude.org",
  holder: visualizationContainer[0],
  parseurl: true,
  nobox: 1,
  noheader: 1,
  genome: "hg38",
  gene: "kras",
  nativetracks: "RefGene",
  tracks: [{
    type: "vcf",
    name: "Clinvar",
    file: "hg38/clinvar.hg38.vcf.gz",
    vcfinfofilter: {
      lst: [
        {
          name: "Clinical significance",
          locusinfo: {
            key: "CLNSIG",
          },
          categories: {
            "Uncertain_significance": {color: "#aaa", label: "Uncertain significance", textcolor: "white"},
            "not_provided": {color: "#ccc", label: "Not provided"},
            "_not_provided": {color: "#ccc", label: "Not provided"},
            "Benign": {color: "#43ac6a", label: "Benign", textcolor: "white"},
            "Benign/Likely_benign": {color: "#43ac6a", label: "Benign/Likely benign", textcolor: "white"},
            "Likely_benign": {color: "#5bc0de", label: "Likely benign", textcolor: "white"},
            "Likely_pathogenic": {color: "#e99002", label: "Likely pathogenic", textcolor: "white"},
            "Pathogenic": {color: "#f04124", label: "Pathogenic", textcolor: "white"},
            "Pathogenic/Likely_pathogenic": {color: "#f04124", label: "Pathogenic/Likely pathogenic", textcolor: "white"},
            "drug_response": {color: "gold", label: "Drug response", textcolor: "white"},
            "_drug_response": {color: "gold", label: "Drug response", textcolor: "white"},
            "Conflicting_interpretations_of_pathogenicity": {color: "#90C3D4", label: "Conflicting interpretations of pathogenicity"},
            "other": {color: "#ccc", label: "Other"},
            "_other": {color: "#ccc", label: "Other"},
            "not_provided": {color: "#ccc", label: "Not provided"},
            "_not_provided": {color: "#ccc", label: "Not provided"},
            "risk_factor": {color: "#ccc", label: "Risk factor"},
            "_risk_factor": {color: "#ccc", label: "Risk factor"},
            "association": {color: "#ccc", label: "Association"},
            "_association": {color: "#ccc", label: "Association"},
            "Affects": {color: "#ccc", label: "Affects"},
            "_Affects": {color: "#ccc", label: "Affects"},
            "protective": {color: "#ccc", label: "Protective"},
            "_protective": {color: "#ccc", label: "Protective"},
          }
        },
        {
          name: "ExAC frequency",
          locusinfo: {key: "AF_EXAC"},
          numericfilter: [{side: "<", value: 0.0001}, {side: "<", value: 0.001}, {side: "<", value: .01}],
        },
        {
          name: "GO-ESP frequency",
          locusinfo: {key: "AF_ESP"},
          numericfilter: [{side: "<", value: 0.0001}, {side: "<", value: 0.001}, {side: "<", value: .01}],
        },
        {
          name: "1000 Genomes frequency",
          locusinfo: {key: "AF_TGP"},
          numericfilter: [{side: "<", value: 0.0001}, {side: "<", value: 0.001}, {side: "<", value: .01}],
        }
      ],
      "setidx4mclass": 0,
      setidx4numeric: 1,
    }
  }
  ]
});

Visualization Code

runproteinpaint({
  host: "https://proteinpaint.stjude.org",
  holder: visualizationContainer[0],
  parseurl: true,
  nobox: 1,
  noheader: 1,
  genome: "hg38",
  gene: "kras",
  nativetracks: "RefGene",
  tracks: [{
    type: "vcf",
    name: "Clinvar",
    file: "hg38/clinvar.hg38.vcf.gz",
    vcfinfofilter: {
      lst: [
        {
          name: "Clinical significance",
          locusinfo: {
            key: "CLNSIG",
          },
          categories: {
            "Uncertain_significance": {color: "#aaa", label: "Uncertain significance", textcolor: "white"},
            "not_provided": {color: "#ccc", label: "Not provided"},
            "_not_provided": {color: "#ccc", label: "Not provided"},
            "Benign": {color: "#43ac6a", label: "Benign", textcolor: "white"},
            "Benign/Likely_benign": {color: "#43ac6a", label: "Benign/Likely benign", textcolor: "white"},
            "Likely_benign": {color: "#5bc0de", label: "Likely benign", textcolor: "white"},
            "Likely_pathogenic": {color: "#e99002", label: "Likely pathogenic", textcolor: "white"},
            "Pathogenic": {color: "#f04124", label: "Pathogenic", textcolor: "white"},
            "Pathogenic/Likely_pathogenic": {color: "#f04124", label: "Pathogenic/Likely pathogenic", textcolor: "white"},
            "drug_response": {color: "gold", label: "Drug response", textcolor: "white"},
            "_drug_response": {color: "gold", label: "Drug response", textcolor: "white"},
            "Conflicting_interpretations_of_pathogenicity": {color: "#90C3D4", label: "Conflicting interpretations of pathogenicity"},
            "other": {color: "#ccc", label: "Other"},
            "_other": {color: "#ccc", label: "Other"},
            "not_provided": {color: "#ccc", label: "Not provided"},
            "_not_provided": {color: "#ccc", label: "Not provided"},
            "risk_factor": {color: "#ccc", label: "Risk factor"},
            "_risk_factor": {color: "#ccc", label: "Risk factor"},
            "association": {color: "#ccc", label: "Association"},
            "_association": {color: "#ccc", label: "Association"},
            "Affects": {color: "#ccc", label: "Affects"},
            "_Affects": {color: "#ccc", label: "Affects"},
            "protective": {color: "#ccc", label: "Protective"},
            "_protective": {color: "#ccc", label: "Protective"},
          }
        },
        {
          name: "ExAC frequency",
          locusinfo: {key: "AF_EXAC"},
          numericfilter: [{side: "<", value: 0.0001}, {side: "<", value: 0.001}, {side: "<", value: .01}],
        },
        {
          name: "GO-ESP frequency",
          locusinfo: {key: "AF_ESP"},
          numericfilter: [{side: "<", value: 0.0001}, {side: "<", value: 0.001}, {side: "<", value: .01}],
        },
        {
          name: "1000 Genomes frequency",
          locusinfo: {key: "AF_TGP"},
          numericfilter: [{side: "<", value: 0.0001}, {side: "<", value: 0.001}, {side: "<", value: .01}],
        }
      ],
      "setidx4mclass": 0,
      setidx4numeric: 1,
    }
  }
  ]
});

GenomePaint VCF Track Example

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Visualization Code