Configuring tracks

All tracks can contain:

• trackId - internal track ID, must be unique
• name - displayed track name
• assemblyNames - an array of assembly names a track is associated with, often just a single assemblyName
• category - (optional) array of categories to display in a hierarchical track selector

Example config.json containing a track config for a BigBed file:

File locations in adapter configs use a { "uri": "..." } object. The "locationType": "UriLocation" field is optional for URI locations and can be omitted — it is only needed when the type cannot be inferred (e.g. local file paths on desktop).

{
  "assemblies": [
    ...the hg19 assembly...
  ],
  "tracks": [
    {
      "type": "FeatureTrack",
      "trackId": "repeats_hg19",
      "name": "Repeats",
      "assemblyNames": ["hg19"],
      "category": ["Annotation"],
      "adapter": {
        "type": "BigBedAdapter",
        "bigBedLocation": {
          "uri": "https://jbrowse.org/genomes/hg19/repeats.bb"
        }
      }
    }
  ]
}

A reduced form is also accepted:

{
  "type": "BigBedAdapter",
  "uri": "https://jbrowse.org/genomes/hg19/repeats.bb"
}

The displays array#

Tracks can include a displays array to configure display-level settings such as height, color callbacks, or which display type is active by default. Each entry targets a specific display type via its displayId.

The displayId convention is {trackId}-{displayType}, for example my_bam_track-LinearAlignmentsDisplay. JBrowse uses this convention internally — if you omit the displays array the defaults are used, but if you provide a displays entry without the correct displayId it will be silently ignored.

{
  "type": "FeatureTrack",
  "trackId": "repeats_hg19",
  "name": "Repeats",
  "assemblyNames": ["hg19"],
  "adapter": {
    "type": "BigBedAdapter",
    "bigBedLocation": { "uri": "https://jbrowse.org/genomes/hg19/repeats.bb" }
  },
  "displays": [
    {
      "type": "LinearBasicDisplay",
      "displayId": "repeats_hg19-LinearBasicDisplay",
      "height": 200,
      "renderer": {
        "type": "SvgFeatureRenderer",
        "color1": "jexl:get(feature,'strand')==1?'blue':'red'"
      }
    }
  ]
}

Common display types and their displayId suffix:

| Track type | Display type | | ---------------------- | ------------------------ | | FeatureTrack | LinearBasicDisplay | | AlignmentsTrack | LinearAlignmentsDisplay | | VariantTrack | LinearVariantDisplay | | MultiQuantitativeTrack | MultiLinearWiggleDisplay | | QuantitativeTrack | LinearWiggleDisplay |

See the config_guides for per-track display options.