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Alignments track

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.

Goes in the tracks array of config.json. See Tracks.

{
  "type": "AlignmentsTrack",
  "trackId": "my_alignments_track",
  "name": "My Alignments",
  "assemblyNames": ["hg19"],
  "adapter": { "type": "BamAdapter", "uri": "https://yourhost/file.bam" },
  "displayDefaults": { "color": { "field": "pairOrientation" }, "height": 250 }
}
jbrowse add-track https://yourhost/file.bam \
  --trackId my_alignments_track \
  --name "My Alignments" \
  --assemblyNames hg19 \
  --displayDefaults '{"color":{"field":"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": { "color": { "field": "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)
  • color, height, featureHeight, filter and the coverage band's scales.y are LinearAlignmentsDisplay slots. Reads draw gray with mismatches marked until color names a field — strand, pairOrientation, insertSize or tags.XX — and baseColor draws modifications or base quality over them; the cookbook has the coloring, grouping and flag-filter recipe
  • unit says what one row stands for, a read or a chain of a read with its mate and split segments; facet stacks one labelled section per value of a read field (pairOrientation, tags.HP); and arcColor picks the pair field the read-connection arcs paint when it is not the reads'

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

See also