Skip to main content

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
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 lists no samples of its own (a MAF track discovering its species from the file) takes the table's rows as its samples