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GWASTrack

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

Example usage

GWASAdapter is a BedTabixAdapter that defaults scoreColumn to neg_log_pvalue. If your BED holds a raw p-value (not -log10 p), point scoreColumn at that column and set scoreTransform: 'negLog10' so it's converted into the Manhattan -log10 p value (use negLog10FromLn for a natural-log p-value, or a jexl:... expression of score such as jexl:-log10(score) for anything else):

{
  type: 'GWASTrack',
  trackId: 'gwas',
  name: 'GWAS results',
  assemblyNames: ['hg38'],
  adapter: {
    type: 'GWASAdapter',
    uri: 'https://example.com/gwas.bed.gz',
    scoreColumn: 'p_value',
    scoreTransform: 'negLog10',
  },
}

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

used for GWAS (Genome-Wide Association Study) tracks with Manhattan plot display

Config slots

These slots are top-level fields of the track config, alongside trackId and name. 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
Inherited from BaseTrack13 slots
name
string = ''		descriptive name of the track, falls back to the trackId when unset
assemblyNames
stringArray = ['assemblyName']		name of the assembly (or assemblies) track belongs to
description
string = ''		a description of the track
category
stringArray = []		the category and sub-categories of a track
metadata
frozen = {}		anything to add about this track
adapter
pluginManager.pluggableConfigSchemaType('adapter')		where this track's data comes from. Its type names the adapter for the file format (BamAdapter, Gff3TabixAdapter, ...) and the rest of the object is that adapter's own slots — see the adapter pages for each. Most adapters also accept a uri shorthand in place of writing their location slots out.
textSearching.indexingAttributes
stringArray = ['Name', 'ID', 'symbol']		list of which feature attributes to index for text searching
textSearching.indexingFeatureTypesToExclude
stringArray = ['CDS', 'exon']		list of feature types to exclude in text search index
textSearching.indexingFeatureTypesToInclude
stringArray = []		The only feature types to index, dropping every other type the file carries. Empty (the default) means no allow list, i.e. index everything indexingFeatureTypesToExclude does not name.

Use this instead of the exclude list when the file draws from a vocabulary you do not control. An NCBI RefSeq GFF3 uses 115 feature types, 80 of them leaf records with nothing to search for — a match is labelled with a bare UUID, a cDNA_match with an MD5, every biological_region with the literal string "biological region" — so a deny list leaks whichever type is added next, while the allow list (gene, pseudogene, and the transcript types) does not grow. Both may be set: this one admits, the exclude list then narrows.

GFF3 only; the GTF and VCF indexers do not filter by type.
textSearching.textSearchAdapter
pluginManager.pluggableConfigSchemaType(
  'text search adapter',
)
a per-track name search index, normally a TrixTextSearchAdapter over what jbrowse text-index --tracks built. Without one, this track's features are only findable through an assembly-wide search adapter.
displays
types.array(pluginManager.pluggableConfigSchemaType('display'))		An array of full display configs, e.g. displays: [{ type: 'LinearBasicDisplay', color: 'green' }]. Each entry names a display type; use this when you need exact control — your own displayId, different settings for two displays, or choosing which display is the default.

For the common case, prefer the displayDefaults shorthand instead — an object of appearance settings (e.g. displayDefaults: { color: 'green' }) that JBrowse routes to whichever display uses each setting, so you don't have to name the display or write the array.

See the track config guide.
formatDetails
FormatDetailsConfigSchemaFactory()		jexl callbacks that add, rewrite or hide fields in this track's feature-details panel. Four slots, listed at FormatDetails, and the same schema exists session-wide as configuration.formatDetails.
formatAbout
FormatAboutConfigSchemaFactory()		jexl callbacks that add, rewrite or hide fields in this track's About dialog. Two slots, listed at FormatAbout, and the same schema exists session-wide as configuration.formatAbout.