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SplitVcfTabixAdapter

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: 'SplitVcfTabixAdapter',
    vcfGzLocationMap: {
      chr1: { uri: 'chr1.vcf.gz' },
      chr2: { uri: 'chr2.vcf.gz' },
    },
    indexLocationMap: {
      chr1: { uri: 'chr1.vcf.gz.tbi' },
      chr2: { uri: 'chr2.vcf.gz.tbi' },
    },
  },
}

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

reads a set of per-chromosome VCF files, keyed by refName, instead of a single combined VCF (useful for large call sets split by chromosome)

Config slots

These slots go inside the track's adapter: "adapter": { "type": "SplitVcfTabixAdapter", ... }. This adapter has no uri shorthand — give it the location slots below. 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
vcfGzLocationMap
frozen = {}		object like {chr1:{uri:'url to file'}}
indexLocationMap
frozen = {}		object like {chr1:{uri:'url to index'}}
indexType
stringEnum (TBI, CSI) = 'TBI'		index flavor for every entry of indexLocationMap — one setting covers them all, so the per-chromosome files have to be indexed the same way. CSI is required for a reference longer than 512 Mb, which TBI cannot address.
samplesTsvLocation
fileLocation = { uri: '/path/to/samples.tsv', locationType: 'UriLocation' }		location of a tab-separated table of per-sample metadata, shared by every file in vcfGzLocationMap. It needs a header row, and its first column must be the sample name exactly as the VCFs spell 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		The same 5 Mb VcfTabixAdapter declares, for the same reason: this adapter implements getRegionByteSize, so its reads are byte-gated, and without a limit of its own the gate falls back to the display config's conservative 1 Mb (resolveByteLimit prefers the adapter's). That gated a split VCF five times tighter than the single-file VCF beside it, on a block-granular tabix estimate that already over-quotes small regions.
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