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VcfAdapter

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

Reads plain-text (non-bgzipped) VCF files. The adapter loads the whole file into memory, so use VcfTabixAdapter for large files.

Example usage

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

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

Config slots

Adapter 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
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