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GWASAdapter

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

Example usage

{
  type: 'GWASTrack',
  trackId: 'my_track',
  name: 'My track',
  assemblyNames: ['hg38'],
  adapter: {
    type: 'GWASAdapter',
    uri: 'https://example.com/summary_stats.txt.gz',
  },
}

summary_stats.txt.gz infers GWASAdapter and GWASTrack 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/summary_stats.txt.gz',
  assemblyNames: ['hg38'],
}

Reading a raw p-value column instead, transformed to -log10(p) at load:

{
  type: 'GWASTrack',
  trackId: 'my_track',
  name: 'My track',
  assemblyNames: ['hg38'],
  adapter: {
    type: 'GWASAdapter',
    uri: 'https://example.com/summary_stats.txt.gz',
    scoreColumn: 'pval',
    scoreTransform: 'negLog10',
  },
}

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

adapter for GWAS results files; a BedTabixAdapter with scoreColumn defaulted to neg_log_pvalue so files load with a sensible Manhattan plot score out of the box

Config slots

These slots go inside the track's adapter: "adapter": { "type": "GWASAdapter", ... }. 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
scoreColumn
string = 'neg_log_pvalue'		BED column to read as the Manhattan plot score
scoreTransform
string = 'none'		transform applied to scoreColumn to produce the Manhattan -log10(p) value: none (column is already -log10, e.g. Pan-UKBB neglog10_pval_*), negLog10 (column is a raw p-value), negLog10FromLn (column is a natural-log p-value, e.g. Pan-UKBB Hail ln P), or a jexl:... expression of score for anything else (e.g. jexl:-log10(score)) — arbitrary but slower than the native modes, so opt-in only
ldAdapter
frozen = null		optional PLINK .ld sub-adapter (PlinkLDAdapter / PlinkLDTabixAdapter) supplying pairwise r² used for LocusZoom-style coloring when the Manhattan display's colorBy is ld; null disables it
Inherited from BedTabixAdapter6 slots
bedGzLocation
fileLocation = { uri: '/path/to/my.bed.gz', locationType: 'UriLocation' }		location of the bgzip-compressed BED, sorted by position. Must be bgzip rather than plain gzip, which tabix cannot index.
columnNames
stringArray = []		List of column names. A column named like a standard BED column is parsed as that column's type (chromStart numeric, blockSizes a numeric list); any other column is text
autoSql
string = ''		The autoSql definition for the data fields in the file
disableGeneHeuristic
boolean = false		Disable the heuristic that auto-detects BED12 features as gene/transcript structures. Useful for files that have BED12-like structure but are not genes (e.g. tandem duplications)
index.indexType
stringEnum (TBI, CSI) = 'TBI'		TBI is the usual tabix output. CSI is required for a reference longer than 512 Mb, which TBI cannot address.
index.location
fileLocation = { uri: '/path/to/my.gz.tbi', locationType: 'UriLocation' }		location of the tabix index. Only needed when it is not named <file>.tbi (or .csi), which is what the uri shorthand assumes.