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VcfTabixAdapter

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

Example usage

The uri shorthand auto-resolves the .tbi index (pass csi: true for a .csi index):

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

variants.vcf.gz infers VcfTabixAdapter 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.gz',
  assemblyNames: ['hg38'],
}

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

Gotcha

TBI cannot index a chromosome longer than 512 Mb, which some plant and animal genomes exceed. Index those with CSI instead: pass csi: true alongside the uri shorthand, or set both index.location and index.indexType: 'CSI' explicitly.

used to load bgzip-compressed, tabix-indexed VCF files

Config slots

These slots go inside the track's adapter: "adapter": { "type": "VcfTabixAdapter", ... }. It also accepts the shorthand keys uri, baseUri, csi 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
vcfGzLocation
fileLocation = { uri: '/path/to/my.vcf.gz', locationType: 'UriLocation' }		location of the bgzip-compressed VCF, sorted by position. Must be bgzip rather than plain gzip, which tabix cannot index.
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.
fetchSizeLimit
number = 5_000_000		Matches the feature-track default (5 Mb): the tabix byte estimate is block-granular (a small region still pulls whole BGZF blocks), so a tighter gate trips on routine variant views. VCF text downloads fast; the feature-density gate remains the backstop for genuinely over-dense views.
advanced
index.indexType
stringEnum (TBI, CSI) = 'TBI'		TBI is the usual tabix output. CSI is required for a reference longer than 512 Mb, which TBI cannot address.
index.location
fileLocation = { uri: '/path/to/my.gz.tbi', locationType: 'UriLocation' }		location of the tabix index. Only needed when it is not named <file>.tbi (or .csi), which is what the uri shorthand assumes.