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Alignments track

TL;DR: point an AlignmentsTrack at a BAM or CRAM with the uri shorthand and the index resolves automatically. Coloring, height, and filtering are slots on the LinearAlignmentsDisplay, set via displayDefaults.

Example AlignmentsTrack config:

{
  "type": "AlignmentsTrack",
  "trackId": "my_alignments_track",
  "name": "My Alignments",
  "assemblyNames": ["hg19"],
  "adapter": {
    "type": "BamAdapter",
    "uri": "https://yourhost/file.bam"
  }
}
jbrowse add-track https://yourhost/file.bam \
  --trackId my_alignments_track \
  --name "My Alignments" \
  --assemblyNames hg19

Adapter options

The uri shorthand above resolves the index for you (<uri>.bai for a BAM, <uri>.crai for a CRAM), so most tracks need nothing else. Add "csi": true alongside uri for a CSI-indexed BAM. See the uri shorthand for when to spell out the location slots, and when CSI is required.

CRAM decodes against the reference sequence; both adapters take their sequenceAdapter from the enclosing assembly automatically.

See the BamAdapter and CramAdapter config docs for all options.

Display options

Display settings (colorBy, height, featureHeight, filterBy, and the coverage autoscale/minScore/maxScore) are slots on the LinearAlignmentsDisplay. By default every read is drawn the same gray with its mismatches marked; colorBy colors the reads by strand, pair orientation, insert size, a tag, and so on. Set one with the track's displayDefaults shorthand:

{
  "type": "AlignmentsTrack",
  "trackId": "my_alignments_track",
  "name": "My Alignments",
  "assemblyNames": ["hg19"],
  "adapter": { "type": "BamAdapter", "uri": "https://yourhost/file.bam" },
  "displayDefaults": { "colorBy": { "type": "pairOrientation" }, "height": 250 }
}
jbrowse add-track https://yourhost/file.bam \
  --trackId my_alignments_track \
  --name "My Alignments" \
  --assemblyNames hg19 \
  --displayDefaults '{"colorBy":{"type":"pairOrientation"},"height":250}'

See the LinearAlignmentsDisplay config docs for the full list of slots. To open a track in a particular state from a link or embedded view, see applying display settings.

See also