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VcfTabixAdapter

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

Reads bgzip-compressed, tabix-indexed VCF files.

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',
  },
}

JBrowse infers VcfTabixAdapter and VariantTrack from variants.vcf.gz, 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'],
}
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.

Config slots

Adapter 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.
index
TabixIndex		The tabix index location and its kind. The uri shorthand derives both, so a config using it states neither.
fetchSizeLimit
number = 5000000		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
samplesTsvLocation
maybeFileLocation		optional tab-separated table of per-sample metadata. It needs a header row, and its first column is the sample name exactly as the adapter spells it: a VCF sample, a MultiWiggle subtrack's name, a MAF species id. Every other column (population, tissue, ...) becomes an attribute of that sample, which the multi-row displays group, sort, color and tooltip rows by; a MAF adapter reads the label, color and assemblyName columns onto its species rows, over its samples entries. The table also narrows the adapter's samples to the ones it lists, and a table naming none of them is an error. An adapter that names no samples (a MAF track discovering its species from the file) takes the table's rows as its samples