LinearVariantDisplay

Auto-generated from the config schema in the source. See the config guide for concepts. Provided by the variants plugin. View source.

Draws a VariantTrack: its records, stacked as a feature track stacks them (records), over one genotype row per sample or per phased haplotype (genotypes). A VCF with no samples draws its records alone. The default display of a VariantTrack.

Example usage#

Minimal VariantTrack config. See the variant track guide for all options:

{
  type: 'VariantTrack',
  trackId: 'cohort',
  name: 'Cohort variants',
  assemblyNames: ['hg38'],
  adapter: {
    type: 'VcfTabixAdapter',
    uri: 'https://example.com/cohort.vcf.gz',
  },
}

Preloading sample metadata: point the adapter's samplesTsvLocation at a TSV whose first column is the sample name and whose other columns are per-sample attributes (e.g. population), then rows.color one of those attributes to color the sidebar rows on load. This is the 1000 Genomes "colored by population" demo config:

{
  type: 'VariantTrack',
  trackId: 'cohort',
  name: 'Cohort variants',
  assemblyNames: ['hg38'],
  adapter: {
    type: 'VcfTabixAdapter',
    uri: 'https://example.com/cohort.vcf.gz',
    samplesTsvLocation: { uri: 'https://example.com/samples.tsv' },
  },
  displays: [
    {
      type: 'LinearVariantDisplay',
      height: 800,
      rows: { color: 'population' },
    },
  ],
}

Phased haplotype rows, one per haplotype of each sample, named HG002 HP1, HG002 HP2. A sample's name stands for its haplotype rows, so the order below puts both of HG002's rows first:

{
  type: 'VariantTrack',
  trackId: 'cohort',
  name: 'Cohort variants',
  assemblyNames: ['hg38'],
  adapter: {
    type: 'VcfTabixAdapter',
    uri: 'https://example.com/cohort.vcf.gz',
  },
  displays: [
    {
      type: 'LinearVariantDisplay',
      height: 400,
      rows: { field: 'haplotype', sort: ['HG002'] },
    },
  ],
}

One equal-width column per variant, tied to the genome by connector lines, for reading a genotype pattern across variants too close together to separate at their positions:

{
  type: 'LinearVariantDisplay',
  variantLayout: 'columns',
}

Related links#

• Adapter: BedpeAdapter
• Adapter: SplitVcfTabixAdapter
• Adapter: StarFusionAdapter
• Adapter: VcfAdapter
• Adapter: VcfTabixAdapter
• State model: runtime API
• Base config: BaseLinearDisplay
• Tutorial: LD across an inversion (mosquitoes)
• Tutorial: Mutation cohort (TCGA)
• User guide: Variant sample rows
• Config guide: Grouping and lane order
• Config guide: Tracks
• Config guide: Variant track
• Developer guide: Custom track and display types

Color channels#

Config slots#

Display slots go on a display entry: "displays": [{ "type": "LinearVariantDisplay", ... }], or in the track's displayDefaults when this is its default display. Slot types (fileLocation, frozen, ...) are explained in the config slot types reference. Slots a base configuration contributes are listed here too, so this table is the whole surface.

{
  type: 'LinearVariantDisplay',
  genotypes: { reference: { show: true } },
}

Retired keys#

An older config may still write these. Each loads without an error, and jbrowse validate reports it as stale.