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VcfAdapter

Auto-generated config schema for the current JBrowse release — see the config guide for concepts. Provided by the variants plugin. View source.

Example usage

{
  type: 'VariantTrack',
  trackId: 'my_track',
  name: 'My track',
  assemblyNames: ['hg38'],
  adapter: {
    type: 'VcfAdapter',
    uri: 'https://example.com/variants.vcf',
  },
}

variants.vcf infers VcfAdapter and VariantTrack on its own, and name defaults to the file name. In a config declaring one assembly, assemblyNames comes from there too — see the shortest track.

{
  trackId: 'my_track',
  uri: 'https://example.com/variants.vcf',
  assemblyNames: ['hg38'],
}

See the Config slots section below for all available configuration fields.

used to load plain-text (non-bgzipped) VCF files. Loads the whole file into memory, so prefer the VcfTabixAdapter for large files.

Config slots

These slots go inside the track's adapter: "adapter": { "type": "VcfAdapter", ... }. It also accepts the shorthand keys uri, baseUri in place of writing a location slot out. 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.

SlotDescription
vcfLocation
fileLocation = { uri: '/path/to/my.vcf', locationType: 'UriLocation' }		location of the VCF file. May be gzipped; it is read and parsed in full on first use, so the whole call set has to fit in memory.
samplesTsvLocation
fileLocation = { uri: '/path/to/samples.tsv', locationType: 'UriLocation' }		location of a tab-separated table of per-sample metadata. It needs a header row, and its first column must be the sample name exactly as the VCF spells it; every other column (population, superpopulation, ...) becomes a value the multi-sample variant displays can group, sort and color their sample rows by.