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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.

{
  "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}'

In JBrowse Desktop, or in any running JBrowse Web session, open a view on this track’s assembly, then File → Open track..., choose Add track from pasted JSON, and paste:

{
  "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 }
}
  • The uri shorthand resolves the index (.bai for a BAM, .crai for a CRAM); add "csi": true for a CSI-indexed BAM (the uri shorthand)
  • CRAM decodes against the reference, and both adapters take their sequenceAdapter from the enclosing assembly, so the track names none (BamAdapter, CramAdapter)
  • colorBy, height, featureHeight, filterBy and the coverage autoscale/minScore/maxScore are LinearAlignmentsDisplay slots. Reads draw gray with mismatches marked until colorBy colors them by strand, pair orientation, insert size or a tag; the cookbook has the coloring, grouping and flag-filter recipe

Applying display settings opens a track in a given state from a link or an embedded view.

See also