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Complex rearrangements and derivative alleles

JBrowse v5 beta

The tutorials target the JBrowse v5 beta, and the v4.3.0 release on the download page lacks some of what they show. To install the beta of JBrowse Web, run npm install -g @jbrowse/cli@next, then jbrowse create jbrowse2 --branch v5.0.0-beta.8. Desktop beta builds are coming soon.

A rearrangement can take several junctions to make, and which genes it joins does not reveal how many. Follow one across every locus it visits in a breakpoint split view, then show the derivative allele assembled from the reads that span it against the reference, as a synteny view.

Prerequisites

On Debian/Ubuntu, apt install samtools minimap2 python3 covers three of those; bedGraphToBigWig is a single static binary from UCSC and node, for the CLI, comes from nodejs.org.

Where the data comes from

Every file but the last comes out of one ONT open-data release and its own wf-somatic-variation run; the last is the multi-platform truth set (Valle-Inclán et al. 2022):

COLO829

COLO829 is a melanoma cell line with a matched normal, COLO829BL, and a community reference for somatic structural-variant calling. The tumor is sequenced deeply enough on ONT R10 that a read crosses a whole rearrangement.

The coverage lanes beside those reads are the same run's mosdepth output in 50 kb windows, repacked as bigWig:

# awk drops the alt and decoy contigs: bedGraphToBigWig rejects a contig absent
# from the chrom.sizes outright, so one leftover row fails the conversion.
gzip -dc COLO829_tumor.regions.bed.gz | sort -k1,1 -k2,2n |
  awk 'NR==FNR{ok[$1];next} ($1 in ok)' hg38.chrom.sizes - > cov.bg
bedGraphToBigWig cov.bg hg38.chrom.sizes COLO829_tumor.coverage.bw

Multi-hop fusions

Fusion callers generally look for one junction joining two genes. Two genes can also be brought together by a series of junctions, and when the reference segments between them are short, the result is indistinguishable at the transcript level from a simple fusion. SplitThreader made this concrete in SK-BR-3 (Nattestad et al. 2018), finding a KLHDC2-SNTB1 fusion that required three variants across three chromosomes. Finding such a chain is a job for an SV interpretation tool; this page is about looking at one once you have it.

Getting a chain to look at

A chain is a claim that one molecule carries several junctions, and deciding which junctions those are takes more than the junction list: copy number, the caller's own clustering, or reads that cross the whole thing. Tools built for that decision are the place to get one.

  • LINX clusters breakends into rearrangement events under eleven rules and chains them under allele-specific copy-number constraints, writing chainId and chainIndex per link (Shale et al. 2022).
  • Severus builds breakpoint graphs from phased tumor and normal long reads and writes a CLUSTERID per complex subgraph into its VCF, which suits the ONT data this page uses.
  • gGnome and JaBbA infer a junction-balanced genome graph whose walks are allelic paths (Hadi et al. 2020).
  • SplitThreader searches a junction graph for the shortest path between two genes, which is the multi-hop fusion question stated directly.

JBrowse itself will follow a chain outward from a record you click — the Follow further breakends at each end option in the breakpoint split view dialog. That walk has only the junction list to go on, so it infers the route from how close breakends sit and stops as soon as two continuations are open. It is a convenience for a callset you have nothing else for, not a substitute for the tools above.

COLO829's der(3) is the chain the rest of this page follows. Three junctions close a triangle across three chromosomes:

chr3:25,359,111  <-> chr12:72,273,112
chr3:25,359,568  <-> chr10:58,717,464
chr10:58,717,662 <-> chr12:72,273,294

The whole derivative path is under a kilobase spread across three chromosomes. The genes involved are RARB on chr3, a tumor suppressor, BICC1 on chr10, and TRHDE on chr12.

Reads at the breakpoints

At the chr3 breakpoints the tumor pileup becomes soft-clipped bases, because every read crossing the junction has its remainder aligned elsewhere. The matched normal at the same locus is clean. Soft clipping is off by default; turn it on from the track menu with Show soft clipping. These pileups are deep enough that the track asks before downloading the window, and Force load approves it for the rest of the session.

Left: COLO829 tumor above COLO829BL normal at the two chr3 breakpoints, soft clipping shown. Tumor reads clip where normal reads read through. Right: the same event as a breakpoint split view over every locus the chain visits.

Following the chain across panels

A breakpoint split view, the right half of the figure above, stacks the loci the chain visits and draws the reads that leave one panel and arrive in another. Add → Breakpoint split view builds a view whose loci you already know, one row per panel. The callset already knows them, so the view can also open from a record. Right-click it in the variant track and choose Open breakpoint split view: one dialog asks for the shape, two stacked panels or one row spanning both breakends, and the window each panel opens at.

A BND names one partner, so the record on its own is two loci. Follow further breakends at each end walks the callset: at each end of the chain it looks for another junction leaving from the same place, and takes it when there is exactly one. On this record that is three panels, because the chr10 breakend has a second junction a couple of hundred bases away whose far end is on chr12. The walk stops at two open continuations, or at one leading back into the chain. The dialog's walk assumes that two junctions leaving one locus belong to one molecule, and the reads are the evidence for that.

Opening the split view from the record itself: right-click the breakend, set the shape and window in the dialog, and get three panels because the chain runs chr3 to chr10 to chr12. Open this view in JBrowse ↗ (large dataset — this session takes a while to load)

The steps behind the figure above, run against your own data.

  1. Open your genome: on the JBrowse Desktop start screen click Open new genome (or Show all available genomes to pick a hosted one).This figure uses hg38.
  2. Add your own track: File → Open track..., then paste a URL or choose a local file.This figure uses the “COLO829_somatic_sv” track.
  3. Drag the bar at the bottom edge of the track to resize it.“COLO829_somatic_sv”.
  4. Add your own track: File → Open track..., then paste a URL or choose a local file.This figure uses the “COLO829_tumor_ont” track.
  5. Drag the bar at the bottom edge of the track to resize it.“COLO829_tumor_ont”.
  6. Track menu → Read height → Super-compact“COLO829_tumor_ont”.
  7. Click Force load in the track's "Zoom in to see features or force load" message.Loads the region even past the byte-size limit, which can be slow.“COLO829_tumor_ont”.
  8. Type your region of interest into the location box and press Enter.This figure is at chr3:25,359,318-25,359,818.

Open this view in JBrowse Desktop ↗

Opens JBrowse Desktop (JBrowse Desktop 5.0+) at this view and saves it as a reopenable session — swap in your own files afterwards.

Nothing happens? Paste this link into Desktop's Open JBrowse Web link... (start screen, or File → Session):

https://jbrowse.org/code/jb2/main/?config=https%3A%2F%2Fjbrowse.org%2Fdemos%2Fcancer_sv%2Fconfig.json&session=spec-%7B%22views%22%3A%5B%7B%22type%22%3A%22LinearGenomeView%22%2C%22assembly%22%3A%22hg38%22%2C%22loc%22%3A%22chr3%3A25%2C359%2C318-25%2C359%2C818%22%2C%22tracks%22%3A%5B%7B%22trackId%22%3A%22COLO829_somatic_sv%22%2C%22height%22%3A130%7D%2C%7B%22trackId%22%3A%22COLO829_tumor_ont%22%2C%22height%22%3A300%2C%22featureHeight%22%3A1%2C%22type%22%3A%22LinearAlignmentsDisplay%22%2C%22forceLoad%22%3Atrue%7D%5D%7D%5D%7D&sessionName=JBrowse+docs%3A+cancer_sv%2Fsplit_view_from_breakend

This session spec pastes after &session=spec- on any JBrowse Web instance.

{
  "views": [
    {
      "type": "LinearGenomeView",
      "assembly": "hg38",
      "loc": "chr3:25,359,318-25,359,818",
      "tracks": [
        {
          "trackId": "COLO829_somatic_sv",
          "height": 130
        },
        {
          "trackId": "COLO829_tumor_ont",
          "height": 300,
          "featureHeight": 1,
          "type": "LinearAlignmentsDisplay",
          "forceLoad": true
        }
      ]
    }
  ]
}

Loaded against config: https://jbrowse.org/demos/cancer_sv/config.json

The same view with jbrowse-anywidget, from the config the figure loads. Swap a track's uri for your own file.

from jbrowse_anywidget import JBrowseApp, fetch_hub

config = fetch_hub("https://jbrowse.org/demos/cancer_sv/config.json")
app = JBrowseApp(
    assemblies=config["assemblies"],
    tracks=config.get("tracks", []),
    views=[
        {
            "type": "LinearGenomeView",
            "assembly": "hg38",
            "loc": "chr3:25,359,318-25,359,818",
            "tracks": [
                {
                    "trackId": "COLO829_somatic_sv",
                    "height": 130
                },
                {
                    "trackId": "COLO829_tumor_ont",
                    "height": 300,
                    "featureHeight": 1,
                    "type": "LinearAlignmentsDisplay",
                    "forceLoad": True
                }
            ]
        }
    ],
)
app  # display the widget

Hand this to a coding agent. It rebuilds the figure above headlessly, and the session file is then the thing to edit — swap an adapter uri for your own file and rerun.

cat > session.json <<'JSON'
{
  "views": [
    {
      "type": "LinearGenomeView",
      "assembly": "hg38",
      "loc": "chr3:25,359,318-25,359,818",
      "tracks": [
        {
          "trackId": "COLO829_somatic_sv",
          "height": 130
        },
        {
          "trackId": "COLO829_tumor_ont",
          "height": 300,
          "featureHeight": 1,
          "type": "LinearAlignmentsDisplay",
          "forceLoad": true
        }
      ]
    }
  ]
}
JSON

npx @jbrowse/capture --instance https://jbrowse.org/code/jb2/main/ \
  --config https://jbrowse.org/demos/cancer_sv/config.json \
  --session session.json -o figure.png

Using JBrowse with AI agents covers the rest: hosted genomes to point it at, and why waiting for the render is the part that goes wrong.

For a single read, right-click it and choose Linear read vs ref. That builds a synteny view with the read as its own assembly along the bottom and every locus it touches along the top, the view Ribbon (Nattestad et al. 2021) introduced.

Stacked panels describe the event in reference coordinates. Laid out along the derivative, it shows the order and orientation of its pieces. The next section rebuilds the allele's sequence and lays the event out along it.

The derivative allele's sequence

The demo carries a der(3) contig: 39,549 bp built from the 29 tumour reads that span all three loci. Every base in it is one those reads carried, which is the property that lets the rest of this section treat it as evidence.

Assembling an allele is an assembler's job. Flye, Shasta and hifiasm all do local assemblies of this kind; pull the reads crossing your loci with samtools view, assemble them, and put the contig through the two commands the tracks below read:

# contigs.fa is the assembler's output for the reads crossing the loci
minimap2 -cx asm5 GRCh38.fa contigs.fa > der3.vs_reference.paf
jbrowse make-pif der3.vs_reference.paf

The published contig aligns to the reference in four blocks:

    derivative       0-32732   + -> chr3:25,326,821-25,359,568
    derivative   32732-32931   + -> chr10:58,717,463-58,717,662
    derivative   32932-33115   - -> chr12:72,273,111-72,273,294
    derivative   33126-39549   - -> chr3:25,352,683-25,359,111

The derivative has four contiguous segments: two chr3 arms in opposite orientations, a foldback, with short pieces of chr10 and chr12 spliced in at the turn. Those two fragments are templated insertions, stretches of other chromosomes captured at a repair junction.

The PAF is a synteny track and the contig is an assembly, so the derivative loads against the reference directly. The BED names which reference interval each stretch of the contig came from, as a feature track on the derivative — a gene track cannot say this, since derivative segments usually sit inside one big intron.

The demo also carries the reference's gene annotation projected through those segments into derivative coordinates, clipped where a junction cut a feature and flipped where a segment is inverted. This allele carries RARB's first coding exon and its start codon, then the 183 bp of chr12 that the second junction splices in, which is TRHDE coding sequence in reverse, then RARB again inverted.

Ribbons below are colored by the reference chromosome they come from. The last segment names the event: an interval the allele has already carried, read back on the other strand, so the derivative turns around on itself. That leaves the stretch in the allele twice in opposite orientations, an inverted duplication, with the two templated inserts at the turn. A fold-back is the first step of a breakage-fusion-bridge cycle.

The read lane under the reference row draws split alignments only, one row per molecule, with the truth set's validated calls above it.

Between the two, each junction is drawn once as an arc joining its two ends, with a short tick at each foot over the sequence that end keeps: ticks pointing away from each other are a deletion-type join, toward each other a duplication-type, and parallel an inversion.

The reconstructed derivative against its three source loci: RefSeq genes, the truth set and the tumor's split reads above, with each junction drawn once as an arc; the same annotation projected onto the allele below, each segment labelled with the interval it came from. Open this view in JBrowse ↗

The steps behind the figure above, run against your own data.

  1. Open your genomes: on the JBrowse Desktop start screen click Open new genome (or Show all available genomes to pick a hosted one), then File → Open genome... for each of the rest.This figure's rows, top to bottom: hg38, der3_RARB_BICC1_TRHDE.
  2. Open the view: Add → Linear synteny view, and set the rows to those assemblies in the import form.
  3. Point the import form at your own file: click the arrow between two rows, choose New track, and paste a URL or pick a local file.A synteny track the session already has is quicker: pick it under **Quick start**, which fills in the rows itself.This figure uses the “der3_vs_hg38” track.
  4. Click Launch.
  5. Click the view's title in its header and enter "Reconstructed derivative allele vs hg38"
  6. Synteny display settings (the sliders button in the view header) → Curved lines (checked)
  7. Synteny view header → palette button → ReferenceThe palette button's tooltip reads "Color by: ...". Reference is offered only in a stacked view of three or more genomes, where there is a shared reference to trace.
  8. Drag the bar below a synteny level to resize it.This figure's level is 88px tall.
  9. Add your own track: open this view's track selector, click + and choose Add track, then paste a URL or choose a local file.Row 1 (hg38) — This figure uses the “ncbi_refseq_hg38” track.
  10. Track menu → Gene glyph → Representative transcriptRow 1 (hg38) · “ncbi_refseq_hg38”.
  11. Drag the bar at the bottom edge of the track to resize it.Row 1 (hg38) · “ncbi_refseq_hg38”.
  12. Track menu → Set feature height → CompactRow 1 (hg38) · “ncbi_refseq_hg38”.
  13. Add your own track: open this view's track selector, click + and choose Add track, then paste a URL or choose a local file. This one needs a VCF file (.vcf).Row 1 (hg38) — This figure uses “COLO829 validated somatic SVs (Valle-Inclán 2022)”.
  14. Drag the bar at the bottom edge of the track to resize it.Row 1 (hg38) · “COLO829 validated somatic SVs (Valle-Inclán 2022)”.
  15. Add your own track: open this view's track selector, click + and choose Add track, then paste a URL or choose a local file.Row 1 (hg38) — This figure uses the “COLO829_tumor_ont” track.
  16. Click Force load in the track's "Zoom in to see features or force load" message.Loads the region even past the byte-size limit, which can be slow.Row 1 (hg38) · “COLO829_tumor_ont”.
  17. Track menu → Filter by... → Split alignments → Only split alignmentsA read filter drops reads in the worker before layout, so it thins the coverage histogram along with the pileup.Row 1 (hg38) · “COLO829_tumor_ont”.
  18. Track menu → Read connections → View as pairs / link supplementary alignments (checked)Row 1 (hg38) · “COLO829_tumor_ont”.
  19. Track menu → Read connections → Use curved connectors (checked)Draws a read's alignments joined by a curve rather than a straight line. Worth it when the two ends sit in different displayed regions, where the curve reads as one read crossing the gap.Row 1 (hg38) · “COLO829_tumor_ont”.
  20. Track menu → Color by... → Supplementary / split reads → Color supplementary alignments by consensus strand (unchecked)Greyed out until "Read connections → View as pairs / link supplementary alignments" is on. It is what classifies a long read's segments against the orientation the chains on screen agree on, so unchecking it drops the red/blue split-segment colouring and the legend rows that go with it.Row 1 (hg38) · “COLO829_tumor_ont”.
  21. Track menu → Read height → Track sizing → Fixed read height + autogrow track heightRow 1 (hg38) · “COLO829_tumor_ont”.
  22. Drag the bar at the bottom edge of the track to resize it.Row 1 (hg38) · “COLO829_tumor_ont”.
  23. Drag the bottom edge of the coverage band to resize it.Row 1 (hg38) · “COLO829_tumor_ont”.
  24. Track menu → Read height → CompactRow 1 (hg38) · “COLO829_tumor_ont”.
  25. Track menu → Read connections → Read arcsRow 1 (hg38) · “COLO829_tumor_ont”.
  26. Drag the handle at the edge of the arc band to resize it (110px here).Its tooltip reads "Drag to resize arcs area"; there is no menu entry for the height.Row 1 (hg38) · “COLO829_tumor_ont”.
  27. Track menu → Show... → Show legend (checked)Row 1 (hg38) · “COLO829_tumor_ont”.
  28. Type your region of interest into the location box and press Enter.Row 1 (hg38) — This figure is at chr3:25350000-25363000 chr10:58716500-58718500 chr12:72272000-72274500.
  29. View menu → Show... → OverlappingRow 1 (hg38).
  30. View menu → Zoom to region / use the location box, then add a highlightThis figure highlights 2 regions; highlights can also be set with the &highlight= URL parameter.Row 1 (hg38).
  31. Add your own track: open this view's track selector, click + and choose Add track, then paste a URL or choose a local file.Row 2 (der3_RARB_BICC1_TRHDE) — This figure uses the “der3_segments” track.
  32. Track menu → Set feature height → CompactRow 2 (der3_RARB_BICC1_TRHDE) · “der3_segments”.
  33. Add your own track: open this view's track selector, click + and choose Add track, then paste a URL or choose a local file. This one needs features defined inline in the config.Row 2 (der3_RARB_BICC1_TRHDE) — This figure uses “Reference genes projected onto the derivative”.
  34. Track menu → Gene glyph → Representative transcriptRow 2 (der3_RARB_BICC1_TRHDE) · “Reference genes projected onto the derivative”.
  35. Drag the bar at the bottom edge of the track to resize it.Row 2 (der3_RARB_BICC1_TRHDE) · “Reference genes projected onto the derivative”.
  36. Track menu → Set feature height → CompactRow 2 (der3_RARB_BICC1_TRHDE) · “Reference genes projected onto the derivative”.
  37. Type your region of interest into the location box and press Enter.Row 2 (der3_RARB_BICC1_TRHDE) — This figure is at der3_RARB_BICC1_TRHDE:22,000-39,549.
  38. View menu → Show... → OffsetRow 2 (der3_RARB_BICC1_TRHDE).

Some settings have no written step yet — see the Session spec tab.

Open this view in JBrowse Desktop ↗

Opens JBrowse Desktop (JBrowse Desktop 5.0+) at this view and saves it as a reopenable session — swap in your own files afterwards.

Nothing happens? Paste this link into Desktop's Open JBrowse Web link... (start screen, or File → Session):

https://jbrowse.org/code/jb2/main/?config=https%3A%2F%2Fjbrowse.org%2Fdemos%2Fcancer_sv%2Fconfig.json&session=spec-%7B%22sessionTracks%22%3A%5B%7B%22type%22%3A%22FeatureTrack%22%2C%22trackId%22%3A%22der3_genes%22%2C%22name%22%3A%22Reference+genes+projected+onto+the+derivative%22%2C%22assemblyNames%22%3A%5B%22der3_RARB_BICC1_TRHDE%22%5D%2C%22adapter%22%3A%7B%22type%22%3A%22FromConfigAdapter%22%2C%22features%22%3A%5B%7B%22uniqueId%22%3A%22RARB.seg0%22%2C%22refName%22%3A%22der3_RARB_BICC1_TRHDE%22%2C%22start%22%3A0%2C%22end%22%3A32732%2C%22strand%22%3A1%2C%22type%22%3A%22gene%22%2C%22name%22%3A%22RARB%22%2C%22subfeatures%22%3A%5B%7B%22uniqueId%22%3A%22NM_001290216.3.seg0%22%2C%22refName%22%3A%22der3_RARB_BICC1_TRHDE%22%2C%22start%22%3A0%2C%22end%22%3A32732%2C%22strand%22%3A1%2C%22type%22%3A%22transcript%22%2C%22name%22%3A%22NM_001290216.3%22%7D%2C%7B%22uniqueId%22%3A%22NM_001290300.2.seg0%22%2C%22refName%22%3A%22der3_RARB_BICC1_TRHDE%22%2C%22start%22%3A13980%2C%22end%22%3A32732%2C%22strand%22%3A1%2C%22type%22%3A%22transcript%22%2C%22name%22%3A%22NM_001290300.2%22%2C%22subfeatures%22%3A%5B%7B%22uniqueId%22%3A%22exon%3ANM_001290300.2.1.seg0%22%2C%22refName%22%3A%22der3_RARB_BICC1_TRHDE%22%2C%22start%22%3A13980%2C%22end%22%3A14070%2C%22strand%22%3A1%2C%22type%22%3A%22exon%22%7D%2C%7B%22uniqueId%22%3A%22CDS%3ANM_001290300.2.1.seg0%22%2C%22refName%22%3A%22der3_RARB_BICC1_TRHDE%22%2C%22start%22%3A14042%2C%22end%22%3A14070%2C%22strand%22%3A1%2C%22type%22%3A%22CDS%22%7D%2C%7B%22uniqueId%22%3A%22start_codon%3ANM_001290300.2.1.seg0%22%2C%22refName%22%3A%22der3_RARB_BICC1_TRHDE%22%2C%22start%22%3A14042%2C%22end%22%3A14045%2C%22strand%22%3A1%2C%22type%22%3A%22start_codon%22%7D%5D%7D%5D%7D%2C%7B%22uniqueId%22%3A%22LOC124906342.seg0%22%2C%22refName%22%3A%22der3_RARB_BICC1_TRHDE%22%2C%22start%22%3A9171%2C%22end%22%3A9237%2C%22strand%22%3A1%2C%22type%22%3A%22gene%22%2C%22name%22%3A%22LOC124906342%22%2C%22subfeatures%22%3A%5B%7B%22uniqueId%22%3A%22XR_007096298.1.seg0%22%2C%22refName%22%3A%22der3_RARB_BICC1_TRHDE%22%2C%22start%22%3A9171%2C%22end%22%3A9237%2C%22strand%22%3A1%2C%22type%22%3A%22transcript%22%2C%22name%22%3A%22XR_007096298.1%22%2C%22subfeatures%22%3A%5B%7B%22uniqueId%22%3A%22exon%3AXR_007096298.1.1.seg0%22%2C%22refName%22%3A%22der3_RARB_BICC1_TRHDE%22%2C%22start%22%3A9171%2C%22end%22%3A9237%2C%22strand%22%3A1%2C%22type%22%3A%22exon%22%7D%5D%7D%5D%7D%2C%7B%22uniqueId%22%3A%22BICC1.seg1%22%2C%22refName%22%3A%22der3_RARB_BICC1_TRHDE%22%2C%22start%22%3A32732%2C%22end%22%3A32931%2C%22strand%22%3A1%2C%22type%22%3A%22gene%22%2C%22name%22%3A%22BICC1%22%2C%22subfeatures%22%3A%5B%7B%22uniqueId%22%3A%22XM_047425780.1.seg1%22%2C%22refName%22%3A%22der3_RARB_BICC1_TRHDE%22%2C%22start%22%3A32732%2C%22end%22%3A32931%2C%22strand%22%3A1%2C%22type%22%3A%22transcript%22%2C%22name%22%3A%22XM_047425780.1%22%7D%5D%7D%2C%7B%22uniqueId%22%3A%22FAM133CP.seg1%22%2C%22refName%22%3A%22der3_RARB_BICC1_TRHDE%22%2C%22start%22%3A32732%2C%22end%22%3A32803%2C%22strand%22%3A1%2C%22type%22%3A%22gene%22%2C%22name%22%3A%22FAM133CP%22%2C%22subfeatures%22%3A%5B%7B%22uniqueId%22%3A%22NR_027508.1.seg1%22%2C%22refName%22%3A%22der3_RARB_BICC1_TRHDE%22%2C%22start%22%3A32732%2C%22end%22%3A32803%2C%22strand%22%3A1%2C%22type%22%3A%22transcript%22%2C%22name%22%3A%22NR_027508.1%22%2C%22subfeatures%22%3A%5B%7B%22uniqueId%22%3A%22exon%3ANR_027508.1.1.seg1%22%2C%22refName%22%3A%22der3_RARB_BICC1_TRHDE%22%2C%22start%22%3A32732%2C%22end%22%3A32803%2C%22strand%22%3A1%2C%22type%22%3A%22exon%22%7D%5D%7D%5D%7D%2C%7B%22uniqueId%22%3A%22TRHDE.seg2%22%2C%22refName%22%3A%22der3_RARB_BICC1_TRHDE%22%2C%22start%22%3A32932%2C%22end%22%3A33115%2C%22strand%22%3A-1%2C%22type%22%3A%22gene%22%2C%22name%22%3A%22TRHDE%22%2C%22subfeatures%22%3A%5B%7B%22uniqueId%22%3A%22XM_017019244.2.seg2%22%2C%22refName%22%3A%22der3_RARB_BICC1_TRHDE%22%2C%22start%22%3A32932%2C%22end%22%3A33115%2C%22strand%22%3A-1%2C%22type%22%3A%22transcript%22%2C%22name%22%3A%22XM_017019244.2%22%7D%2C%7B%22uniqueId%22%3A%22XM_005268819.6.seg2%22%2C%22refName%22%3A%22der3_RARB_BICC1_TRHDE%22%2C%22start%22%3A32932%2C%22end%22%3A33115%2C%22strand%22%3A-1%2C%22type%22%3A%22transcript%22%2C%22name%22%3A%22XM_005268819.6%22%2C%22subfeatures%22%3A%5B%7B%22uniqueId%22%3A%22exon%3AXM_005268819.6.1.seg2%22%2C%22refName%22%3A%22der3_RARB_BICC1_TRHDE%22%2C%22start%22%3A32932%2C%22end%22%3A33115%2C%22strand%22%3A-1%2C%22type%22%3A%22exon%22%7D%2C%7B%22uniqueId%22%3A%22CDS%3AXM_005268819.6.1.seg2%22%2C%22refName%22%3A%22der3_RARB_BICC1_TRHDE%22%2C%22start%22%3A32932%2C%22end%22%3A33115%2C%22strand%22%3A-1%2C%22type%22%3A%22CDS%22%7D%5D%7D%5D%7D%2C%7B%22uniqueId%22%3A%22TRHDE-AS1.seg2%22%2C%22refName%22%3A%22der3_RARB_BICC1_TRHDE%22%2C%22start%22%3A32932%2C%22end%22%3A33115%2C%22strand%22%3A1%2C%22type%22%3A%22gene%22%2C%22name%22%3A%22TRHDE-AS1%22%2C%22subfeatures%22%3A%5B%7B%22uniqueId%22%3A%22NR_026837.1.seg2%22%2C%22refName%22%3A%22der3_RARB_BICC1_TRHDE%22%2C%22start%22%3A32932%2C%22end%22%3A33115%2C%22strand%22%3A1%2C%22type%22%3A%22transcript%22%2C%22name%22%3A%22NR_026837.1%22%2C%22subfeatures%22%3A%5B%7B%22uniqueId%22%3A%22exon%3ANR_026837.1.1.seg2%22%2C%22refName%22%3A%22der3_RARB_BICC1_TRHDE%22%2C%22start%22%3A32932%2C%22end%22%3A33115%2C%22strand%22%3A1%2C%22type%22%3A%22exon%22%7D%5D%7D%5D%7D%2C%7B%22uniqueId%22%3A%22RARB.seg3%22%2C%22refName%22%3A%22der3_RARB_BICC1_TRHDE%22%2C%22start%22%3A33126%2C%22end%22%3A39549%2C%22strand%22%3A-1%2C%22type%22%3A%22gene%22%2C%22name%22%3A%22RARB%22%2C%22subfeatures%22%3A%5B%7B%22uniqueId%22%3A%22NM_001290216.3.seg3%22%2C%22refName%22%3A%22der3_RARB_BICC1_TRHDE%22%2C%22start%22%3A33126%2C%22end%22%3A39549%2C%22strand%22%3A-1%2C%22type%22%3A%22transcript%22%2C%22name%22%3A%22NM_001290216.3%22%7D%5D%7D%5D%7D%7D%2C%7B%22type%22%3A%22VariantTrack%22%2C%22trackId%22%3A%22COLO829_truth_set%22%2C%22name%22%3A%22COLO829+validated+somatic+SVs+%28Valle-Incl%C3%A1n+2022%29%22%2C%22assemblyNames%22%3A%5B%22hg38%22%5D%2C%22adapter%22%3A%7B%22type%22%3A%22VcfAdapter%22%2C%22vcfLocation%22%3A%7B%22uri%22%3A%22https%3A%2F%2Fzenodo.org%2Fapi%2Frecords%2F4716169%2Ffiles%2Ftruthset_somaticSVs_COLO829_hg38lifted.vcf%2Fcontent%22%7D%7D%7D%5D%2C%22views%22%3A%5B%7B%22type%22%3A%22LinearSyntenyView%22%2C%22displayName%22%3A%22Reconstructed+derivative+allele+vs+hg38%22%2C%22views%22%3A%5B%7B%22assembly%22%3A%22hg38%22%2C%22trackLabels%22%3A%22overlapping%22%2C%22loc%22%3A%22chr3%3A25350000-25363000+chr10%3A58716500-58718500+chr12%3A72272000-72274500%22%2C%22highlight%22%3A%5B%7B%22refName%22%3A%22chr3%22%2C%22assemblyName%22%3A%22hg38%22%2C%22label%22%3A%22junctions%22%2C%22start%22%3A25358000%2C%22end%22%3A25360600%7D%2C%7B%22refName%22%3A%22chr3%22%2C%22assemblyName%22%3A%22hg38%22%2C%22label%22%3A%22not+in+the+allele%22%2C%22start%22%3A25360600%2C%22end%22%3A25363000%2C%22color%22%3A%22rgba%2860%2C65%2C72%2C0.10%29%22%7D%5D%2C%22tracks%22%3A%5B%7B%22trackId%22%3A%22ncbi_refseq_hg38%22%2C%22geneGlyphMode%22%3A%22longestCoding%22%2C%22height%22%3A50%2C%22type%22%3A%22LinearBasicDisplay%22%2C%22displayMode%22%3A%22compact%22%7D%2C%7B%22trackId%22%3A%22COLO829_truth_set%22%2C%22displayMode%22%3A%22collapsed%22%2C%22height%22%3A30%7D%2C%7B%22trackId%22%3A%22COLO829_tumor_ont%22%2C%22type%22%3A%22LinearAlignmentsDisplay%22%2C%22forceLoad%22%3Atrue%2C%22filterBy%22%3A%7B%22split%22%3A%22only%22%7D%2C%22linkedReads%22%3A%22normal%22%2C%22showBezierConnections%22%3Atrue%2C%22flipStrandLongReadChains%22%3Afalse%2C%22heightMode%22%3A%22grow%22%2C%22height%22%3A200%2C%22coverageHeight%22%3A30%2C%22featureHeight%22%3A3%2C%22readConnections%22%3A%22arc%22%2C%22readConnectionsHeight%22%3A110%2C%22showLegend%22%3Atrue%7D%5D%7D%2C%7B%22assembly%22%3A%22der3_RARB_BICC1_TRHDE%22%2C%22loc%22%3A%22der3_RARB_BICC1_TRHDE%3A22%2C000-39%2C549%22%2C%22trackLabels%22%3A%22offset%22%2C%22tracks%22%3A%5B%7B%22trackId%22%3A%22der3_segments%22%2C%22type%22%3A%22LinearBasicDisplay%22%2C%22displayMode%22%3A%22compact%22%7D%2C%7B%22trackId%22%3A%22der3_genes%22%2C%22geneGlyphMode%22%3A%22longestCoding%22%2C%22height%22%3A74%2C%22type%22%3A%22LinearBasicDisplay%22%2C%22displayMode%22%3A%22compact%22%7D%5D%7D%5D%2C%22tracks%22%3A%5B%5B%22der3_vs_hg38%22%5D%5D%2C%22drawCurves%22%3Atrue%2C%22colorBy%22%3A%7B%22field%22%3A%22reference%22%7D%2C%22levelHeights%22%3A%5B88%5D%7D%5D%7D&sessionName=JBrowse+docs%3A+cancer_sv%2Fderivative_synteny

A figure adds its tracks to one session. The jbrowse CLI writes the same tracks into a config.json instead, where every session that opens it has them: add-track where flags cover the whole track, add-track-json where they do not.

jbrowse add-track-json '{
  "type": "FeatureTrack",
  "trackId": "der3_genes",
  "name": "Reference genes projected onto the derivative",
  "assemblyNames": [
    "der3_RARB_BICC1_TRHDE"
  ],
  "adapter": {
    "type": "FromConfigAdapter",
    "features": [
      {
        "uniqueId": "RARB.seg0",
        "refName": "der3_RARB_BICC1_TRHDE",
        "start": 0,
        "end": 32732,
        "strand": 1,
        "type": "gene",
        "name": "RARB",
        "subfeatures": [
          {
            "uniqueId": "NM_001290216.3.seg0",
            "refName": "der3_RARB_BICC1_TRHDE",
            "start": 0,
            "end": 32732,
            "strand": 1,
            "type": "transcript",
            "name": "NM_001290216.3"
          },
          {
            "uniqueId": "NM_001290300.2.seg0",
            "refName": "der3_RARB_BICC1_TRHDE",
            "start": 13980,
            "end": 32732,
            "strand": 1,
            "type": "transcript",
            "name": "NM_001290300.2",
            "subfeatures": [
              {
                "uniqueId": "exon:NM_001290300.2.1.seg0",
                "refName": "der3_RARB_BICC1_TRHDE",
                "start": 13980,
                "end": 14070,
                "strand": 1,
                "type": "exon"
              },
              {
                "uniqueId": "CDS:NM_001290300.2.1.seg0",
                "refName": "der3_RARB_BICC1_TRHDE",
                "start": 14042,
                "end": 14070,
                "strand": 1,
                "type": "CDS"
              },
              {
                "uniqueId": "start_codon:NM_001290300.2.1.seg0",
                "refName": "der3_RARB_BICC1_TRHDE",
                "start": 14042,
                "end": 14045,
                "strand": 1,
                "type": "start_codon"
              }
            ]
          }
        ]
      },
      {
        "uniqueId": "LOC124906342.seg0",
        "refName": "der3_RARB_BICC1_TRHDE",
        "start": 9171,
        "end": 9237,
        "strand": 1,
        "type": "gene",
        "name": "LOC124906342",
        "subfeatures": [
          {
            "uniqueId": "XR_007096298.1.seg0",
            "refName": "der3_RARB_BICC1_TRHDE",
            "start": 9171,
            "end": 9237,
            "strand": 1,
            "type": "transcript",
            "name": "XR_007096298.1",
            "subfeatures": [
              {
                "uniqueId": "exon:XR_007096298.1.1.seg0",
                "refName": "der3_RARB_BICC1_TRHDE",
                "start": 9171,
                "end": 9237,
                "strand": 1,
                "type": "exon"
              }
            ]
          }
        ]
      },
      {
        "uniqueId": "BICC1.seg1",
        "refName": "der3_RARB_BICC1_TRHDE",
        "start": 32732,
        "end": 32931,
        "strand": 1,
        "type": "gene",
        "name": "BICC1",
        "subfeatures": [
          {
            "uniqueId": "XM_047425780.1.seg1",
            "refName": "der3_RARB_BICC1_TRHDE",
            "start": 32732,
            "end": 32931,
            "strand": 1,
            "type": "transcript",
            "name": "XM_047425780.1"
          }
        ]
      },
      {
        "uniqueId": "FAM133CP.seg1",
        "refName": "der3_RARB_BICC1_TRHDE",
        "start": 32732,
        "end": 32803,
        "strand": 1,
        "type": "gene",
        "name": "FAM133CP",
        "subfeatures": [
          {
            "uniqueId": "NR_027508.1.seg1",
            "refName": "der3_RARB_BICC1_TRHDE",
            "start": 32732,
            "end": 32803,
            "strand": 1,
            "type": "transcript",
            "name": "NR_027508.1",
            "subfeatures": [
              {
                "uniqueId": "exon:NR_027508.1.1.seg1",
                "refName": "der3_RARB_BICC1_TRHDE",
                "start": 32732,
                "end": 32803,
                "strand": 1,
                "type": "exon"
              }
            ]
          }
        ]
      },
      {
        "uniqueId": "TRHDE.seg2",
        "refName": "der3_RARB_BICC1_TRHDE",
        "start": 32932,
        "end": 33115,
        "strand": -1,
        "type": "gene",
        "name": "TRHDE",
        "subfeatures": [
          {
            "uniqueId": "XM_017019244.2.seg2",
            "refName": "der3_RARB_BICC1_TRHDE",
            "start": 32932,
            "end": 33115,
            "strand": -1,
            "type": "transcript",
            "name": "XM_017019244.2"
          },
          {
            "uniqueId": "XM_005268819.6.seg2",
            "refName": "der3_RARB_BICC1_TRHDE",
            "start": 32932,
            "end": 33115,
            "strand": -1,
            "type": "transcript",
            "name": "XM_005268819.6",
            "subfeatures": [
              {
                "uniqueId": "exon:XM_005268819.6.1.seg2",
                "refName": "der3_RARB_BICC1_TRHDE",
                "start": 32932,
                "end": 33115,
                "strand": -1,
                "type": "exon"
              },
              {
                "uniqueId": "CDS:XM_005268819.6.1.seg2",
                "refName": "der3_RARB_BICC1_TRHDE",
                "start": 32932,
                "end": 33115,
                "strand": -1,
                "type": "CDS"
              }
            ]
          }
        ]
      },
      {
        "uniqueId": "TRHDE-AS1.seg2",
        "refName": "der3_RARB_BICC1_TRHDE",
        "start": 32932,
        "end": 33115,
        "strand": 1,
        "type": "gene",
        "name": "TRHDE-AS1",
        "subfeatures": [
          {
            "uniqueId": "NR_026837.1.seg2",
            "refName": "der3_RARB_BICC1_TRHDE",
            "start": 32932,
            "end": 33115,
            "strand": 1,
            "type": "transcript",
            "name": "NR_026837.1",
            "subfeatures": [
              {
                "uniqueId": "exon:NR_026837.1.1.seg2",
                "refName": "der3_RARB_BICC1_TRHDE",
                "start": 32932,
                "end": 33115,
                "strand": 1,
                "type": "exon"
              }
            ]
          }
        ]
      },
      {
        "uniqueId": "RARB.seg3",
        "refName": "der3_RARB_BICC1_TRHDE",
        "start": 33126,
        "end": 39549,
        "strand": -1,
        "type": "gene",
        "name": "RARB",
        "subfeatures": [
          {
            "uniqueId": "NM_001290216.3.seg3",
            "refName": "der3_RARB_BICC1_TRHDE",
            "start": 33126,
            "end": 39549,
            "strand": -1,
            "type": "transcript",
            "name": "NM_001290216.3"
          }
        ]
      }
    ]
  }
}'

jbrowse add-track-json '{
  "type": "VariantTrack",
  "trackId": "COLO829_truth_set",
  "name": "COLO829 validated somatic SVs (Valle-Inclán 2022)",
  "assemblyNames": [
    "hg38"
  ],
  "adapter": {
    "type": "VcfAdapter",
    "vcfLocation": {
      "uri": "https://zenodo.org/api/records/4716169/files/truthset_somaticSVs_COLO829_hg38lifted.vcf/content"
    }
  }
}'

Run these where the config.json is, or add --out <dir>, and point each uri at your own file. The config needs der3_RARB_BICC1_TRHDE, hg38 already — jbrowse add-assembly adds yours. The location and the settings the steps carry are session state rather than track config — that half is the Session spec tab, or jbrowse set-default-session.

This session spec pastes after &session=spec- on any JBrowse Web instance.

{
  "sessionTracks": [
    {
      "type": "FeatureTrack",
      "trackId": "der3_genes",
      "name": "Reference genes projected onto the derivative",
      "assemblyNames": [
        "der3_RARB_BICC1_TRHDE"
      ],
      "adapter": {
        "type": "FromConfigAdapter",
        "features": [
          {
            "uniqueId": "RARB.seg0",
            "refName": "der3_RARB_BICC1_TRHDE",
            "start": 0,
            "end": 32732,
            "strand": 1,
            "type": "gene",
            "name": "RARB",
            "subfeatures": [
              {
                "uniqueId": "NM_001290216.3.seg0",
                "refName": "der3_RARB_BICC1_TRHDE",
                "start": 0,
                "end": 32732,
                "strand": 1,
                "type": "transcript",
                "name": "NM_001290216.3"
              },
              {
                "uniqueId": "NM_001290300.2.seg0",
                "refName": "der3_RARB_BICC1_TRHDE",
                "start": 13980,
                "end": 32732,
                "strand": 1,
                "type": "transcript",
                "name": "NM_001290300.2",
                "subfeatures": [
                  {
                    "uniqueId": "exon:NM_001290300.2.1.seg0",
                    "refName": "der3_RARB_BICC1_TRHDE",
                    "start": 13980,
                    "end": 14070,
                    "strand": 1,
                    "type": "exon"
                  },
                  {
                    "uniqueId": "CDS:NM_001290300.2.1.seg0",
                    "refName": "der3_RARB_BICC1_TRHDE",
                    "start": 14042,
                    "end": 14070,
                    "strand": 1,
                    "type": "CDS"
                  },
                  {
                    "uniqueId": "start_codon:NM_001290300.2.1.seg0",
                    "refName": "der3_RARB_BICC1_TRHDE",
                    "start": 14042,
                    "end": 14045,
                    "strand": 1,
                    "type": "start_codon"
                  }
                ]
              }
            ]
          },
          {
            "uniqueId": "LOC124906342.seg0",
            "refName": "der3_RARB_BICC1_TRHDE",
            "start": 9171,
            "end": 9237,
            "strand": 1,
            "type": "gene",
            "name": "LOC124906342",
            "subfeatures": [
              {
                "uniqueId": "XR_007096298.1.seg0",
                "refName": "der3_RARB_BICC1_TRHDE",
                "start": 9171,
                "end": 9237,
                "strand": 1,
                "type": "transcript",
                "name": "XR_007096298.1",
                "subfeatures": [
                  {
                    "uniqueId": "exon:XR_007096298.1.1.seg0",
                    "refName": "der3_RARB_BICC1_TRHDE",
                    "start": 9171,
                    "end": 9237,
                    "strand": 1,
                    "type": "exon"
                  }
                ]
              }
            ]
          },
          {
            "uniqueId": "BICC1.seg1",
            "refName": "der3_RARB_BICC1_TRHDE",
            "start": 32732,
            "end": 32931,
            "strand": 1,
            "type": "gene",
            "name": "BICC1",
            "subfeatures": [
              {
                "uniqueId": "XM_047425780.1.seg1",
                "refName": "der3_RARB_BICC1_TRHDE",
                "start": 32732,
                "end": 32931,
                "strand": 1,
                "type": "transcript",
                "name": "XM_047425780.1"
              }
            ]
          },
          {
            "uniqueId": "FAM133CP.seg1",
            "refName": "der3_RARB_BICC1_TRHDE",
            "start": 32732,
            "end": 32803,
            "strand": 1,
            "type": "gene",
            "name": "FAM133CP",
            "subfeatures": [
              {
                "uniqueId": "NR_027508.1.seg1",
                "refName": "der3_RARB_BICC1_TRHDE",
                "start": 32732,
                "end": 32803,
                "strand": 1,
                "type": "transcript",
                "name": "NR_027508.1",
                "subfeatures": [
                  {
                    "uniqueId": "exon:NR_027508.1.1.seg1",
                    "refName": "der3_RARB_BICC1_TRHDE",
                    "start": 32732,
                    "end": 32803,
                    "strand": 1,
                    "type": "exon"
                  }
                ]
              }
            ]
          },
          {
            "uniqueId": "TRHDE.seg2",
            "refName": "der3_RARB_BICC1_TRHDE",
            "start": 32932,
            "end": 33115,
            "strand": -1,
            "type": "gene",
            "name": "TRHDE",
            "subfeatures": [
              {
                "uniqueId": "XM_017019244.2.seg2",
                "refName": "der3_RARB_BICC1_TRHDE",
                "start": 32932,
                "end": 33115,
                "strand": -1,
                "type": "transcript",
                "name": "XM_017019244.2"
              },
              {
                "uniqueId": "XM_005268819.6.seg2",
                "refName": "der3_RARB_BICC1_TRHDE",
                "start": 32932,
                "end": 33115,
                "strand": -1,
                "type": "transcript",
                "name": "XM_005268819.6",
                "subfeatures": [
                  {
                    "uniqueId": "exon:XM_005268819.6.1.seg2",
                    "refName": "der3_RARB_BICC1_TRHDE",
                    "start": 32932,
                    "end": 33115,
                    "strand": -1,
                    "type": "exon"
                  },
                  {
                    "uniqueId": "CDS:XM_005268819.6.1.seg2",
                    "refName": "der3_RARB_BICC1_TRHDE",
                    "start": 32932,
                    "end": 33115,
                    "strand": -1,
                    "type": "CDS"
                  }
                ]
              }
            ]
          },
          {
            "uniqueId": "TRHDE-AS1.seg2",
            "refName": "der3_RARB_BICC1_TRHDE",
            "start": 32932,
            "end": 33115,
            "strand": 1,
            "type": "gene",
            "name": "TRHDE-AS1",
            "subfeatures": [
              {
                "uniqueId": "NR_026837.1.seg2",
                "refName": "der3_RARB_BICC1_TRHDE",
                "start": 32932,
                "end": 33115,
                "strand": 1,
                "type": "transcript",
                "name": "NR_026837.1",
                "subfeatures": [
                  {
                    "uniqueId": "exon:NR_026837.1.1.seg2",
                    "refName": "der3_RARB_BICC1_TRHDE",
                    "start": 32932,
                    "end": 33115,
                    "strand": 1,
                    "type": "exon"
                  }
                ]
              }
            ]
          },
          {
            "uniqueId": "RARB.seg3",
            "refName": "der3_RARB_BICC1_TRHDE",
            "start": 33126,
            "end": 39549,
            "strand": -1,
            "type": "gene",
            "name": "RARB",
            "subfeatures": [
              {
                "uniqueId": "NM_001290216.3.seg3",
                "refName": "der3_RARB_BICC1_TRHDE",
                "start": 33126,
                "end": 39549,
                "strand": -1,
                "type": "transcript",
                "name": "NM_001290216.3"
              }
            ]
          }
        ]
      }
    },
    {
      "type": "VariantTrack",
      "trackId": "COLO829_truth_set",
      "name": "COLO829 validated somatic SVs (Valle-Inclán 2022)",
      "assemblyNames": [
        "hg38"
      ],
      "adapter": {
        "type": "VcfAdapter",
        "vcfLocation": {
          "uri": "https://zenodo.org/api/records/4716169/files/truthset_somaticSVs_COLO829_hg38lifted.vcf/content"
        }
      }
    }
  ],
  "views": [
    {
      "type": "LinearSyntenyView",
      "displayName": "Reconstructed derivative allele vs hg38",
      "views": [
        {
          "assembly": "hg38",
          "trackLabels": "overlapping",
          "loc": "chr3:25350000-25363000 chr10:58716500-58718500 chr12:72272000-72274500",
          "highlight": [
            {
              "refName": "chr3",
              "assemblyName": "hg38",
              "label": "junctions",
              "start": 25358000,
              "end": 25360600
            },
            {
              "refName": "chr3",
              "assemblyName": "hg38",
              "label": "not in the allele",
              "start": 25360600,
              "end": 25363000,
              "color": "rgba(60,65,72,0.10)"
            }
          ],
          "tracks": [
            {
              "trackId": "ncbi_refseq_hg38",
              "geneGlyphMode": "longestCoding",
              "height": 50,
              "type": "LinearBasicDisplay",
              "displayMode": "compact"
            },
            {
              "trackId": "COLO829_truth_set",
              "displayMode": "collapsed",
              "height": 30
            },
            {
              "trackId": "COLO829_tumor_ont",
              "type": "LinearAlignmentsDisplay",
              "forceLoad": true,
              "filterBy": {
                "split": "only"
              },
              "linkedReads": "normal",
              "showBezierConnections": true,
              "flipStrandLongReadChains": false,
              "heightMode": "grow",
              "height": 200,
              "coverageHeight": 30,
              "featureHeight": 3,
              "readConnections": "arc",
              "readConnectionsHeight": 110,
              "showLegend": true
            }
          ]
        },
        {
          "assembly": "der3_RARB_BICC1_TRHDE",
          "loc": "der3_RARB_BICC1_TRHDE:22,000-39,549",
          "trackLabels": "offset",
          "tracks": [
            {
              "trackId": "der3_segments",
              "type": "LinearBasicDisplay",
              "displayMode": "compact"
            },
            {
              "trackId": "der3_genes",
              "geneGlyphMode": "longestCoding",
              "height": 74,
              "type": "LinearBasicDisplay",
              "displayMode": "compact"
            }
          ]
        }
      ],
      "tracks": [
        [
          "der3_vs_hg38"
        ]
      ],
      "drawCurves": true,
      "colorBy": {
        "field": "reference"
      },
      "levelHeights": [
        88
      ]
    }
  ]
}

Loaded against config: https://jbrowse.org/demos/cancer_sv/config.json

The same view with jbrowse-anywidget, from the config the figure loads. Swap a track's uri for your own file.

from jbrowse_anywidget import JBrowseApp, fetch_hub

config = fetch_hub("https://jbrowse.org/demos/cancer_sv/config.json")
app = JBrowseApp(
    assemblies=config["assemblies"],
    tracks=config.get("tracks", []) + [
        {
            "type": "FeatureTrack",
            "trackId": "der3_genes",
            "name": "Reference genes projected onto the derivative",
            "assemblyNames": [
                "der3_RARB_BICC1_TRHDE"
            ],
            "adapter": {
                "type": "FromConfigAdapter",
                "features": [
                    {
                        "uniqueId": "RARB.seg0",
                        "refName": "der3_RARB_BICC1_TRHDE",
                        "start": 0,
                        "end": 32732,
                        "strand": 1,
                        "type": "gene",
                        "name": "RARB",
                        "subfeatures": [
                            {
                                "uniqueId": "NM_001290216.3.seg0",
                                "refName": "der3_RARB_BICC1_TRHDE",
                                "start": 0,
                                "end": 32732,
                                "strand": 1,
                                "type": "transcript",
                                "name": "NM_001290216.3"
                            },
                            {
                                "uniqueId": "NM_001290300.2.seg0",
                                "refName": "der3_RARB_BICC1_TRHDE",
                                "start": 13980,
                                "end": 32732,
                                "strand": 1,
                                "type": "transcript",
                                "name": "NM_001290300.2",
                                "subfeatures": [
                                    {
                                        "uniqueId": "exon:NM_001290300.2.1.seg0",
                                        "refName": "der3_RARB_BICC1_TRHDE",
                                        "start": 13980,
                                        "end": 14070,
                                        "strand": 1,
                                        "type": "exon"
                                    },
                                    {
                                        "uniqueId": "CDS:NM_001290300.2.1.seg0",
                                        "refName": "der3_RARB_BICC1_TRHDE",
                                        "start": 14042,
                                        "end": 14070,
                                        "strand": 1,
                                        "type": "CDS"
                                    },
                                    {
                                        "uniqueId": "start_codon:NM_001290300.2.1.seg0",
                                        "refName": "der3_RARB_BICC1_TRHDE",
                                        "start": 14042,
                                        "end": 14045,
                                        "strand": 1,
                                        "type": "start_codon"
                                    }
                                ]
                            }
                        ]
                    },
                    {
                        "uniqueId": "LOC124906342.seg0",
                        "refName": "der3_RARB_BICC1_TRHDE",
                        "start": 9171,
                        "end": 9237,
                        "strand": 1,
                        "type": "gene",
                        "name": "LOC124906342",
                        "subfeatures": [
                            {
                                "uniqueId": "XR_007096298.1.seg0",
                                "refName": "der3_RARB_BICC1_TRHDE",
                                "start": 9171,
                                "end": 9237,
                                "strand": 1,
                                "type": "transcript",
                                "name": "XR_007096298.1",
                                "subfeatures": [
                                    {
                                        "uniqueId": "exon:XR_007096298.1.1.seg0",
                                        "refName": "der3_RARB_BICC1_TRHDE",
                                        "start": 9171,
                                        "end": 9237,
                                        "strand": 1,
                                        "type": "exon"
                                    }
                                ]
                            }
                        ]
                    },
                    {
                        "uniqueId": "BICC1.seg1",
                        "refName": "der3_RARB_BICC1_TRHDE",
                        "start": 32732,
                        "end": 32931,
                        "strand": 1,
                        "type": "gene",
                        "name": "BICC1",
                        "subfeatures": [
                            {
                                "uniqueId": "XM_047425780.1.seg1",
                                "refName": "der3_RARB_BICC1_TRHDE",
                                "start": 32732,
                                "end": 32931,
                                "strand": 1,
                                "type": "transcript",
                                "name": "XM_047425780.1"
                            }
                        ]
                    },
                    {
                        "uniqueId": "FAM133CP.seg1",
                        "refName": "der3_RARB_BICC1_TRHDE",
                        "start": 32732,
                        "end": 32803,
                        "strand": 1,
                        "type": "gene",
                        "name": "FAM133CP",
                        "subfeatures": [
                            {
                                "uniqueId": "NR_027508.1.seg1",
                                "refName": "der3_RARB_BICC1_TRHDE",
                                "start": 32732,
                                "end": 32803,
                                "strand": 1,
                                "type": "transcript",
                                "name": "NR_027508.1",
                                "subfeatures": [
                                    {
                                        "uniqueId": "exon:NR_027508.1.1.seg1",
                                        "refName": "der3_RARB_BICC1_TRHDE",
                                        "start": 32732,
                                        "end": 32803,
                                        "strand": 1,
                                        "type": "exon"
                                    }
                                ]
                            }
                        ]
                    },
                    {
                        "uniqueId": "TRHDE.seg2",
                        "refName": "der3_RARB_BICC1_TRHDE",
                        "start": 32932,
                        "end": 33115,
                        "strand": -1,
                        "type": "gene",
                        "name": "TRHDE",
                        "subfeatures": [
                            {
                                "uniqueId": "XM_017019244.2.seg2",
                                "refName": "der3_RARB_BICC1_TRHDE",
                                "start": 32932,
                                "end": 33115,
                                "strand": -1,
                                "type": "transcript",
                                "name": "XM_017019244.2"
                            },
                            {
                                "uniqueId": "XM_005268819.6.seg2",
                                "refName": "der3_RARB_BICC1_TRHDE",
                                "start": 32932,
                                "end": 33115,
                                "strand": -1,
                                "type": "transcript",
                                "name": "XM_005268819.6",
                                "subfeatures": [
                                    {
                                        "uniqueId": "exon:XM_005268819.6.1.seg2",
                                        "refName": "der3_RARB_BICC1_TRHDE",
                                        "start": 32932,
                                        "end": 33115,
                                        "strand": -1,
                                        "type": "exon"
                                    },
                                    {
                                        "uniqueId": "CDS:XM_005268819.6.1.seg2",
                                        "refName": "der3_RARB_BICC1_TRHDE",
                                        "start": 32932,
                                        "end": 33115,
                                        "strand": -1,
                                        "type": "CDS"
                                    }
                                ]
                            }
                        ]
                    },
                    {
                        "uniqueId": "TRHDE-AS1.seg2",
                        "refName": "der3_RARB_BICC1_TRHDE",
                        "start": 32932,
                        "end": 33115,
                        "strand": 1,
                        "type": "gene",
                        "name": "TRHDE-AS1",
                        "subfeatures": [
                            {
                                "uniqueId": "NR_026837.1.seg2",
                                "refName": "der3_RARB_BICC1_TRHDE",
                                "start": 32932,
                                "end": 33115,
                                "strand": 1,
                                "type": "transcript",
                                "name": "NR_026837.1",
                                "subfeatures": [
                                    {
                                        "uniqueId": "exon:NR_026837.1.1.seg2",
                                        "refName": "der3_RARB_BICC1_TRHDE",
                                        "start": 32932,
                                        "end": 33115,
                                        "strand": 1,
                                        "type": "exon"
                                    }
                                ]
                            }
                        ]
                    },
                    {
                        "uniqueId": "RARB.seg3",
                        "refName": "der3_RARB_BICC1_TRHDE",
                        "start": 33126,
                        "end": 39549,
                        "strand": -1,
                        "type": "gene",
                        "name": "RARB",
                        "subfeatures": [
                            {
                                "uniqueId": "NM_001290216.3.seg3",
                                "refName": "der3_RARB_BICC1_TRHDE",
                                "start": 33126,
                                "end": 39549,
                                "strand": -1,
                                "type": "transcript",
                                "name": "NM_001290216.3"
                            }
                        ]
                    }
                ]
            }
        },
        {
            "type": "VariantTrack",
            "trackId": "COLO829_truth_set",
            "name": "COLO829 validated somatic SVs (Valle-Inclán 2022)",
            "assemblyNames": [
                "hg38"
            ],
            "adapter": {
                "type": "VcfAdapter",
                "vcfLocation": {
                    "uri": "https://zenodo.org/api/records/4716169/files/truthset_somaticSVs_COLO829_hg38lifted.vcf/content"
                }
            }
        }
    ],
    views=[
        {
            "type": "LinearSyntenyView",
            "displayName": "Reconstructed derivative allele vs hg38",
            "views": [
                {
                    "assembly": "hg38",
                    "trackLabels": "overlapping",
                    "loc": "chr3:25350000-25363000 chr10:58716500-58718500 chr12:72272000-72274500",
                    "highlight": [
                        {
                            "refName": "chr3",
                            "assemblyName": "hg38",
                            "label": "junctions",
                            "start": 25358000,
                            "end": 25360600
                        },
                        {
                            "refName": "chr3",
                            "assemblyName": "hg38",
                            "label": "not in the allele",
                            "start": 25360600,
                            "end": 25363000,
                            "color": "rgba(60,65,72,0.10)"
                        }
                    ],
                    "tracks": [
                        {
                            "trackId": "ncbi_refseq_hg38",
                            "geneGlyphMode": "longestCoding",
                            "height": 50,
                            "type": "LinearBasicDisplay",
                            "displayMode": "compact"
                        },
                        {
                            "trackId": "COLO829_truth_set",
                            "displayMode": "collapsed",
                            "height": 30
                        },
                        {
                            "trackId": "COLO829_tumor_ont",
                            "type": "LinearAlignmentsDisplay",
                            "forceLoad": True,
                            "filterBy": {
                                "split": "only"
                            },
                            "linkedReads": "normal",
                            "showBezierConnections": True,
                            "flipStrandLongReadChains": False,
                            "heightMode": "grow",
                            "height": 200,
                            "coverageHeight": 30,
                            "featureHeight": 3,
                            "readConnections": "arc",
                            "readConnectionsHeight": 110,
                            "showLegend": True
                        }
                    ]
                },
                {
                    "assembly": "der3_RARB_BICC1_TRHDE",
                    "loc": "der3_RARB_BICC1_TRHDE:22,000-39,549",
                    "trackLabels": "offset",
                    "tracks": [
                        {
                            "trackId": "der3_segments",
                            "type": "LinearBasicDisplay",
                            "displayMode": "compact"
                        },
                        {
                            "trackId": "der3_genes",
                            "geneGlyphMode": "longestCoding",
                            "height": 74,
                            "type": "LinearBasicDisplay",
                            "displayMode": "compact"
                        }
                    ]
                }
            ],
            "tracks": [
                [
                    "der3_vs_hg38"
                ]
            ],
            "drawCurves": True,
            "colorBy": {
                "field": "reference"
            },
            "levelHeights": [
                88
            ]
        }
    ],
)
app  # display the widget

Hand this to a coding agent. It rebuilds the figure above headlessly, and the session file is then the thing to edit — swap an adapter uri for your own file and rerun.

cat > session.json <<'JSON'
{
  "sessionTracks": [
    {
      "type": "FeatureTrack",
      "trackId": "der3_genes",
      "name": "Reference genes projected onto the derivative",
      "assemblyNames": [
        "der3_RARB_BICC1_TRHDE"
      ],
      "adapter": {
        "type": "FromConfigAdapter",
        "features": [
          {
            "uniqueId": "RARB.seg0",
            "refName": "der3_RARB_BICC1_TRHDE",
            "start": 0,
            "end": 32732,
            "strand": 1,
            "type": "gene",
            "name": "RARB",
            "subfeatures": [
              {
                "uniqueId": "NM_001290216.3.seg0",
                "refName": "der3_RARB_BICC1_TRHDE",
                "start": 0,
                "end": 32732,
                "strand": 1,
                "type": "transcript",
                "name": "NM_001290216.3"
              },
              {
                "uniqueId": "NM_001290300.2.seg0",
                "refName": "der3_RARB_BICC1_TRHDE",
                "start": 13980,
                "end": 32732,
                "strand": 1,
                "type": "transcript",
                "name": "NM_001290300.2",
                "subfeatures": [
                  {
                    "uniqueId": "exon:NM_001290300.2.1.seg0",
                    "refName": "der3_RARB_BICC1_TRHDE",
                    "start": 13980,
                    "end": 14070,
                    "strand": 1,
                    "type": "exon"
                  },
                  {
                    "uniqueId": "CDS:NM_001290300.2.1.seg0",
                    "refName": "der3_RARB_BICC1_TRHDE",
                    "start": 14042,
                    "end": 14070,
                    "strand": 1,
                    "type": "CDS"
                  },
                  {
                    "uniqueId": "start_codon:NM_001290300.2.1.seg0",
                    "refName": "der3_RARB_BICC1_TRHDE",
                    "start": 14042,
                    "end": 14045,
                    "strand": 1,
                    "type": "start_codon"
                  }
                ]
              }
            ]
          },
          {
            "uniqueId": "LOC124906342.seg0",
            "refName": "der3_RARB_BICC1_TRHDE",
            "start": 9171,
            "end": 9237,
            "strand": 1,
            "type": "gene",
            "name": "LOC124906342",
            "subfeatures": [
              {
                "uniqueId": "XR_007096298.1.seg0",
                "refName": "der3_RARB_BICC1_TRHDE",
                "start": 9171,
                "end": 9237,
                "strand": 1,
                "type": "transcript",
                "name": "XR_007096298.1",
                "subfeatures": [
                  {
                    "uniqueId": "exon:XR_007096298.1.1.seg0",
                    "refName": "der3_RARB_BICC1_TRHDE",
                    "start": 9171,
                    "end": 9237,
                    "strand": 1,
                    "type": "exon"
                  }
                ]
              }
            ]
          },
          {
            "uniqueId": "BICC1.seg1",
            "refName": "der3_RARB_BICC1_TRHDE",
            "start": 32732,
            "end": 32931,
            "strand": 1,
            "type": "gene",
            "name": "BICC1",
            "subfeatures": [
              {
                "uniqueId": "XM_047425780.1.seg1",
                "refName": "der3_RARB_BICC1_TRHDE",
                "start": 32732,
                "end": 32931,
                "strand": 1,
                "type": "transcript",
                "name": "XM_047425780.1"
              }
            ]
          },
          {
            "uniqueId": "FAM133CP.seg1",
            "refName": "der3_RARB_BICC1_TRHDE",
            "start": 32732,
            "end": 32803,
            "strand": 1,
            "type": "gene",
            "name": "FAM133CP",
            "subfeatures": [
              {
                "uniqueId": "NR_027508.1.seg1",
                "refName": "der3_RARB_BICC1_TRHDE",
                "start": 32732,
                "end": 32803,
                "strand": 1,
                "type": "transcript",
                "name": "NR_027508.1",
                "subfeatures": [
                  {
                    "uniqueId": "exon:NR_027508.1.1.seg1",
                    "refName": "der3_RARB_BICC1_TRHDE",
                    "start": 32732,
                    "end": 32803,
                    "strand": 1,
                    "type": "exon"
                  }
                ]
              }
            ]
          },
          {
            "uniqueId": "TRHDE.seg2",
            "refName": "der3_RARB_BICC1_TRHDE",
            "start": 32932,
            "end": 33115,
            "strand": -1,
            "type": "gene",
            "name": "TRHDE",
            "subfeatures": [
              {
                "uniqueId": "XM_017019244.2.seg2",
                "refName": "der3_RARB_BICC1_TRHDE",
                "start": 32932,
                "end": 33115,
                "strand": -1,
                "type": "transcript",
                "name": "XM_017019244.2"
              },
              {
                "uniqueId": "XM_005268819.6.seg2",
                "refName": "der3_RARB_BICC1_TRHDE",
                "start": 32932,
                "end": 33115,
                "strand": -1,
                "type": "transcript",
                "name": "XM_005268819.6",
                "subfeatures": [
                  {
                    "uniqueId": "exon:XM_005268819.6.1.seg2",
                    "refName": "der3_RARB_BICC1_TRHDE",
                    "start": 32932,
                    "end": 33115,
                    "strand": -1,
                    "type": "exon"
                  },
                  {
                    "uniqueId": "CDS:XM_005268819.6.1.seg2",
                    "refName": "der3_RARB_BICC1_TRHDE",
                    "start": 32932,
                    "end": 33115,
                    "strand": -1,
                    "type": "CDS"
                  }
                ]
              }
            ]
          },
          {
            "uniqueId": "TRHDE-AS1.seg2",
            "refName": "der3_RARB_BICC1_TRHDE",
            "start": 32932,
            "end": 33115,
            "strand": 1,
            "type": "gene",
            "name": "TRHDE-AS1",
            "subfeatures": [
              {
                "uniqueId": "NR_026837.1.seg2",
                "refName": "der3_RARB_BICC1_TRHDE",
                "start": 32932,
                "end": 33115,
                "strand": 1,
                "type": "transcript",
                "name": "NR_026837.1",
                "subfeatures": [
                  {
                    "uniqueId": "exon:NR_026837.1.1.seg2",
                    "refName": "der3_RARB_BICC1_TRHDE",
                    "start": 32932,
                    "end": 33115,
                    "strand": 1,
                    "type": "exon"
                  }
                ]
              }
            ]
          },
          {
            "uniqueId": "RARB.seg3",
            "refName": "der3_RARB_BICC1_TRHDE",
            "start": 33126,
            "end": 39549,
            "strand": -1,
            "type": "gene",
            "name": "RARB",
            "subfeatures": [
              {
                "uniqueId": "NM_001290216.3.seg3",
                "refName": "der3_RARB_BICC1_TRHDE",
                "start": 33126,
                "end": 39549,
                "strand": -1,
                "type": "transcript",
                "name": "NM_001290216.3"
              }
            ]
          }
        ]
      }
    },
    {
      "type": "VariantTrack",
      "trackId": "COLO829_truth_set",
      "name": "COLO829 validated somatic SVs (Valle-Inclán 2022)",
      "assemblyNames": [
        "hg38"
      ],
      "adapter": {
        "type": "VcfAdapter",
        "vcfLocation": {
          "uri": "https://zenodo.org/api/records/4716169/files/truthset_somaticSVs_COLO829_hg38lifted.vcf/content"
        }
      }
    }
  ],
  "views": [
    {
      "type": "LinearSyntenyView",
      "displayName": "Reconstructed derivative allele vs hg38",
      "views": [
        {
          "assembly": "hg38",
          "trackLabels": "overlapping",
          "loc": "chr3:25350000-25363000 chr10:58716500-58718500 chr12:72272000-72274500",
          "highlight": [
            {
              "refName": "chr3",
              "assemblyName": "hg38",
              "label": "junctions",
              "start": 25358000,
              "end": 25360600
            },
            {
              "refName": "chr3",
              "assemblyName": "hg38",
              "label": "not in the allele",
              "start": 25360600,
              "end": 25363000,
              "color": "rgba(60,65,72,0.10)"
            }
          ],
          "tracks": [
            {
              "trackId": "ncbi_refseq_hg38",
              "geneGlyphMode": "longestCoding",
              "height": 50,
              "type": "LinearBasicDisplay",
              "displayMode": "compact"
            },
            {
              "trackId": "COLO829_truth_set",
              "displayMode": "collapsed",
              "height": 30
            },
            {
              "trackId": "COLO829_tumor_ont",
              "type": "LinearAlignmentsDisplay",
              "forceLoad": true,
              "filterBy": {
                "split": "only"
              },
              "linkedReads": "normal",
              "showBezierConnections": true,
              "flipStrandLongReadChains": false,
              "heightMode": "grow",
              "height": 200,
              "coverageHeight": 30,
              "featureHeight": 3,
              "readConnections": "arc",
              "readConnectionsHeight": 110,
              "showLegend": true
            }
          ]
        },
        {
          "assembly": "der3_RARB_BICC1_TRHDE",
          "loc": "der3_RARB_BICC1_TRHDE:22,000-39,549",
          "trackLabels": "offset",
          "tracks": [
            {
              "trackId": "der3_segments",
              "type": "LinearBasicDisplay",
              "displayMode": "compact"
            },
            {
              "trackId": "der3_genes",
              "geneGlyphMode": "longestCoding",
              "height": 74,
              "type": "LinearBasicDisplay",
              "displayMode": "compact"
            }
          ]
        }
      ],
      "tracks": [
        [
          "der3_vs_hg38"
        ]
      ],
      "drawCurves": true,
      "colorBy": {
        "field": "reference"
      },
      "levelHeights": [
        88
      ]
    }
  ]
}
JSON

npx @jbrowse/capture --instance https://jbrowse.org/code/jb2/main/ \
  --config https://jbrowse.org/demos/cancer_sv/config.json \
  --session session.json -o figure.png

Using JBrowse with AI agents covers the rest: hosted genomes to point it at, and why waiting for the render is the part that goes wrong.

Checking the reconstruction

Zoomed to the kilobase holding the junctions, the two inserts are the same width as the arms either side. Against hg38 every split read stops at a junction, and the truth set has a validated call at each place they stop. Realigned against the derivative, most of the same reads cross all four junctions in one alignment. They are the reads the consensus was polished from, so that shows they agree with each other; the truth set, called from other platforms, is the independent check.

Each hg38 window runs past the segment the allele takes, so the bare reference on either side of the reads is sequence the allele does not include. That lane draws split alignments only, and its coverage band counts the reads carrying a junction, stepping down as each arm runs out.

The stitching at base scale: chr3 runs out, chr10 follows, then chr12 inverted, then chr3 resumes backwards. Above, the truth set's validated calls over the same molecules against hg38, split alignments only, each row stopping at a call with a connector to the piece it continues on; below, the allele's segments over the reads realigned to them. Open this view in JBrowse ↗

The steps behind the figure above, run against your own data.

  1. Open your genomes: on the JBrowse Desktop start screen click Open new genome (or Show all available genomes to pick a hosted one), then File → Open genome... for each of the rest.This figure's rows, top to bottom: hg38, der3_RARB_BICC1_TRHDE.
  2. Open the view: Add → Linear synteny view, and set the rows to those assemblies in the import form.
  3. Point the import form at your own file: click the arrow between two rows, choose New track, and paste a URL or pick a local file.A synteny track the session already has is quicker: pick it under **Quick start**, which fills in the rows itself.This figure uses the “der3_vs_hg38” track.
  4. Click Launch.
  5. Click the view's title in its header and enter "Two templated inserts join the chr3 arms"
  6. Synteny display settings (the sliders button in the view header) → Curved lines (checked)
  7. Drag the bar below a synteny level to resize it.This figure's level is 140px tall.
  8. Add your own track: open this view's track selector, click + and choose Add track, then paste a URL or choose a local file.Row 1 (hg38) — This figure uses the “ncbi_refseq_hg38” track.
  9. Track menu → Gene glyph → Representative transcriptRow 1 (hg38) · “ncbi_refseq_hg38”.
  10. Drag the bar at the bottom edge of the track to resize it.Row 1 (hg38) · “ncbi_refseq_hg38”.
  11. Add your own track: open this view's track selector, click + and choose Add track, then paste a URL or choose a local file. This one needs a VCF file (.vcf).Row 1 (hg38) — This figure uses “COLO829 validated somatic SVs (Valle-Inclán 2022)”.
  12. Drag the bar at the bottom edge of the track to resize it.Row 1 (hg38) · “COLO829 validated somatic SVs (Valle-Inclán 2022)”.
  13. Add your own track: open this view's track selector, click + and choose Add track, then paste a URL or choose a local file.Row 1 (hg38) — This figure uses the “COLO829_tumor_ont” track.
  14. Click Force load in the track's "Zoom in to see features or force load" message.Loads the region even past the byte-size limit, which can be slow.Row 1 (hg38) · “COLO829_tumor_ont”.
  15. Track menu → Filter by... → Split alignments → Only split alignmentsA read filter drops reads in the worker before layout, so it thins the coverage histogram along with the pileup.Row 1 (hg38) · “COLO829_tumor_ont”.
  16. Track menu → Read connections → View as pairs / link supplementary alignments (checked)Row 1 (hg38) · “COLO829_tumor_ont”.
  17. Track menu → Read connections → Use curved connectors (checked)Draws a read's alignments joined by a curve rather than a straight line. Worth it when the two ends sit in different displayed regions, where the curve reads as one read crossing the gap.Row 1 (hg38) · “COLO829_tumor_ont”.
  18. Track menu → Read height → Track sizing → Fixed read height + autogrow track heightRow 1 (hg38) · “COLO829_tumor_ont”.
  19. Drag the bar at the bottom edge of the track to resize it.Row 1 (hg38) · “COLO829_tumor_ont”.
  20. Track menu → Read height → Custom... → 5pxRow 1 (hg38) · “COLO829_tumor_ont”.
  21. Track menu → Color by... → Supplementary / split reads → Color supplementary alignments by consensus strand (unchecked)Greyed out until "Read connections → View as pairs / link supplementary alignments" is on. It is what classifies a long read's segments against the orientation the chains on screen agree on, so unchecking it drops the red/blue split-segment colouring and the legend rows that go with it.Row 1 (hg38) · “COLO829_tumor_ont”.
  22. Track menu → Show... → Show legend (checked)Row 1 (hg38) · “COLO829_tumor_ont”.
  23. Track menu → Show... → Show coverage (checked)Row 1 (hg38) · “COLO829_tumor_ont”.
  24. Drag the bottom edge of the coverage band to resize it.Row 1 (hg38) · “COLO829_tumor_ont”.
  25. Track menu → Read connections → Read arcsRow 1 (hg38) · “COLO829_tumor_ont”.
  26. Type your region of interest into the location box and press Enter.Row 1 (hg38) — This figure is at chr3:25358500-25360100 chr10:58717200-58717920 chr12:72272880-72273520.
  27. Add your own track: open this view's track selector, click + and choose Add track, then paste a URL or choose a local file.Row 2 (der3_RARB_BICC1_TRHDE) — This figure uses the “der3_segments” track.
  28. Add your own track: open this view's track selector, click + and choose Add track, then paste a URL or choose a local file. This one needs features defined inline in the config.Row 2 (der3_RARB_BICC1_TRHDE) — This figure uses “Reference genes projected onto the derivative”.
  29. Track menu → Gene glyph → Representative transcriptRow 2 (der3_RARB_BICC1_TRHDE) · “Reference genes projected onto the derivative”.
  30. Drag the bar at the bottom edge of the track to resize it.Row 2 (der3_RARB_BICC1_TRHDE) · “Reference genes projected onto the derivative”.
  31. Add your own track: open this view's track selector, click + and choose Add track, then paste a URL or choose a local file.Row 2 (der3_RARB_BICC1_TRHDE) — This figure uses the “reads_vs_der3” track.
  32. Track menu → Read height → Track sizing → Fixed read height + autogrow track heightRow 2 (der3_RARB_BICC1_TRHDE) · “reads_vs_der3”.
  33. Drag the bar at the bottom edge of the track to resize it.Row 2 (der3_RARB_BICC1_TRHDE) · “reads_vs_der3”.
  34. Track menu → Read height → Custom... → 5pxRow 2 (der3_RARB_BICC1_TRHDE) · “reads_vs_der3”.
  35. Track menu → Color by... → Supplementary / split reads → Color supplementary alignments by consensus strand (unchecked)Greyed out until "Read connections → View as pairs / link supplementary alignments" is on. It is what classifies a long read's segments against the orientation the chains on screen agree on, so unchecking it drops the red/blue split-segment colouring and the legend rows that go with it.Row 2 (der3_RARB_BICC1_TRHDE) · “reads_vs_der3”.
  36. Drag the bottom edge of the coverage band to resize it.Row 2 (der3_RARB_BICC1_TRHDE) · “reads_vs_der3”.
  37. Track menu → Read connections → View as pairs / link supplementary alignments (checked)Row 2 (der3_RARB_BICC1_TRHDE) · “reads_vs_der3”.
  38. Track menu → Filter by... → Edit filters...Row 2 (der3_RARB_BICC1_TRHDE) · “reads_vs_der3”.
  39. Type your region of interest into the location box and press Enter.Row 2 (der3_RARB_BICC1_TRHDE) — This figure is at der3_RARB_BICC1_TRHDE:32,300-33,400.
  40. View menu → Show... → Show amino acids when zoomed in (unchecked)Row 2 (der3_RARB_BICC1_TRHDE).

Some settings have no written step yet — see the Session spec tab.

Open this view in JBrowse Desktop ↗

Opens JBrowse Desktop (JBrowse Desktop 5.0+) at this view and saves it as a reopenable session — swap in your own files afterwards.

Nothing happens? Paste this link into Desktop's Open JBrowse Web link... (start screen, or File → Session):

https://jbrowse.org/code/jb2/main/?config=https%3A%2F%2Fjbrowse.org%2Fdemos%2Fcancer_sv%2Fconfig.json&session=spec-%7B%22sessionTracks%22%3A%5B%7B%22type%22%3A%22FeatureTrack%22%2C%22trackId%22%3A%22der3_genes%22%2C%22name%22%3A%22Reference+genes+projected+onto+the+derivative%22%2C%22assemblyNames%22%3A%5B%22der3_RARB_BICC1_TRHDE%22%5D%2C%22adapter%22%3A%7B%22type%22%3A%22FromConfigAdapter%22%2C%22features%22%3A%5B%7B%22uniqueId%22%3A%22RARB.seg0%22%2C%22refName%22%3A%22der3_RARB_BICC1_TRHDE%22%2C%22start%22%3A0%2C%22end%22%3A32732%2C%22strand%22%3A1%2C%22type%22%3A%22gene%22%2C%22name%22%3A%22RARB%22%2C%22subfeatures%22%3A%5B%7B%22uniqueId%22%3A%22NM_001290216.3.seg0%22%2C%22refName%22%3A%22der3_RARB_BICC1_TRHDE%22%2C%22start%22%3A0%2C%22end%22%3A32732%2C%22strand%22%3A1%2C%22type%22%3A%22transcript%22%2C%22name%22%3A%22NM_001290216.3%22%7D%2C%7B%22uniqueId%22%3A%22NM_001290300.2.seg0%22%2C%22refName%22%3A%22der3_RARB_BICC1_TRHDE%22%2C%22start%22%3A13980%2C%22end%22%3A32732%2C%22strand%22%3A1%2C%22type%22%3A%22transcript%22%2C%22name%22%3A%22NM_001290300.2%22%2C%22subfeatures%22%3A%5B%7B%22uniqueId%22%3A%22exon%3ANM_001290300.2.1.seg0%22%2C%22refName%22%3A%22der3_RARB_BICC1_TRHDE%22%2C%22start%22%3A13980%2C%22end%22%3A14070%2C%22strand%22%3A1%2C%22type%22%3A%22exon%22%7D%2C%7B%22uniqueId%22%3A%22CDS%3ANM_001290300.2.1.seg0%22%2C%22refName%22%3A%22der3_RARB_BICC1_TRHDE%22%2C%22start%22%3A14042%2C%22end%22%3A14070%2C%22strand%22%3A1%2C%22type%22%3A%22CDS%22%7D%2C%7B%22uniqueId%22%3A%22start_codon%3ANM_001290300.2.1.seg0%22%2C%22refName%22%3A%22der3_RARB_BICC1_TRHDE%22%2C%22start%22%3A14042%2C%22end%22%3A14045%2C%22strand%22%3A1%2C%22type%22%3A%22start_codon%22%7D%5D%7D%5D%7D%2C%7B%22uniqueId%22%3A%22LOC124906342.seg0%22%2C%22refName%22%3A%22der3_RARB_BICC1_TRHDE%22%2C%22start%22%3A9171%2C%22end%22%3A9237%2C%22strand%22%3A1%2C%22type%22%3A%22gene%22%2C%22name%22%3A%22LOC124906342%22%2C%22subfeatures%22%3A%5B%7B%22uniqueId%22%3A%22XR_007096298.1.seg0%22%2C%22refName%22%3A%22der3_RARB_BICC1_TRHDE%22%2C%22start%22%3A9171%2C%22end%22%3A9237%2C%22strand%22%3A1%2C%22type%22%3A%22transcript%22%2C%22name%22%3A%22XR_007096298.1%22%2C%22subfeatures%22%3A%5B%7B%22uniqueId%22%3A%22exon%3AXR_007096298.1.1.seg0%22%2C%22refName%22%3A%22der3_RARB_BICC1_TRHDE%22%2C%22start%22%3A9171%2C%22end%22%3A9237%2C%22strand%22%3A1%2C%22type%22%3A%22exon%22%7D%5D%7D%5D%7D%2C%7B%22uniqueId%22%3A%22BICC1.seg1%22%2C%22refName%22%3A%22der3_RARB_BICC1_TRHDE%22%2C%22start%22%3A32732%2C%22end%22%3A32931%2C%22strand%22%3A1%2C%22type%22%3A%22gene%22%2C%22name%22%3A%22BICC1%22%2C%22subfeatures%22%3A%5B%7B%22uniqueId%22%3A%22XM_047425780.1.seg1%22%2C%22refName%22%3A%22der3_RARB_BICC1_TRHDE%22%2C%22start%22%3A32732%2C%22end%22%3A32931%2C%22strand%22%3A1%2C%22type%22%3A%22transcript%22%2C%22name%22%3A%22XM_047425780.1%22%7D%5D%7D%2C%7B%22uniqueId%22%3A%22FAM133CP.seg1%22%2C%22refName%22%3A%22der3_RARB_BICC1_TRHDE%22%2C%22start%22%3A32732%2C%22end%22%3A32803%2C%22strand%22%3A1%2C%22type%22%3A%22gene%22%2C%22name%22%3A%22FAM133CP%22%2C%22subfeatures%22%3A%5B%7B%22uniqueId%22%3A%22NR_027508.1.seg1%22%2C%22refName%22%3A%22der3_RARB_BICC1_TRHDE%22%2C%22start%22%3A32732%2C%22end%22%3A32803%2C%22strand%22%3A1%2C%22type%22%3A%22transcript%22%2C%22name%22%3A%22NR_027508.1%22%2C%22subfeatures%22%3A%5B%7B%22uniqueId%22%3A%22exon%3ANR_027508.1.1.seg1%22%2C%22refName%22%3A%22der3_RARB_BICC1_TRHDE%22%2C%22start%22%3A32732%2C%22end%22%3A32803%2C%22strand%22%3A1%2C%22type%22%3A%22exon%22%7D%5D%7D%5D%7D%2C%7B%22uniqueId%22%3A%22TRHDE.seg2%22%2C%22refName%22%3A%22der3_RARB_BICC1_TRHDE%22%2C%22start%22%3A32932%2C%22end%22%3A33115%2C%22strand%22%3A-1%2C%22type%22%3A%22gene%22%2C%22name%22%3A%22TRHDE%22%2C%22subfeatures%22%3A%5B%7B%22uniqueId%22%3A%22XM_017019244.2.seg2%22%2C%22refName%22%3A%22der3_RARB_BICC1_TRHDE%22%2C%22start%22%3A32932%2C%22end%22%3A33115%2C%22strand%22%3A-1%2C%22type%22%3A%22transcript%22%2C%22name%22%3A%22XM_017019244.2%22%7D%2C%7B%22uniqueId%22%3A%22XM_005268819.6.seg2%22%2C%22refName%22%3A%22der3_RARB_BICC1_TRHDE%22%2C%22start%22%3A32932%2C%22end%22%3A33115%2C%22strand%22%3A-1%2C%22type%22%3A%22transcript%22%2C%22name%22%3A%22XM_005268819.6%22%2C%22subfeatures%22%3A%5B%7B%22uniqueId%22%3A%22exon%3AXM_005268819.6.1.seg2%22%2C%22refName%22%3A%22der3_RARB_BICC1_TRHDE%22%2C%22start%22%3A32932%2C%22end%22%3A33115%2C%22strand%22%3A-1%2C%22type%22%3A%22exon%22%7D%2C%7B%22uniqueId%22%3A%22CDS%3AXM_005268819.6.1.seg2%22%2C%22refName%22%3A%22der3_RARB_BICC1_TRHDE%22%2C%22start%22%3A32932%2C%22end%22%3A33115%2C%22strand%22%3A-1%2C%22type%22%3A%22CDS%22%7D%5D%7D%5D%7D%2C%7B%22uniqueId%22%3A%22TRHDE-AS1.seg2%22%2C%22refName%22%3A%22der3_RARB_BICC1_TRHDE%22%2C%22start%22%3A32932%2C%22end%22%3A33115%2C%22strand%22%3A1%2C%22type%22%3A%22gene%22%2C%22name%22%3A%22TRHDE-AS1%22%2C%22subfeatures%22%3A%5B%7B%22uniqueId%22%3A%22NR_026837.1.seg2%22%2C%22refName%22%3A%22der3_RARB_BICC1_TRHDE%22%2C%22start%22%3A32932%2C%22end%22%3A33115%2C%22strand%22%3A1%2C%22type%22%3A%22transcript%22%2C%22name%22%3A%22NR_026837.1%22%2C%22subfeatures%22%3A%5B%7B%22uniqueId%22%3A%22exon%3ANR_026837.1.1.seg2%22%2C%22refName%22%3A%22der3_RARB_BICC1_TRHDE%22%2C%22start%22%3A32932%2C%22end%22%3A33115%2C%22strand%22%3A1%2C%22type%22%3A%22exon%22%7D%5D%7D%5D%7D%2C%7B%22uniqueId%22%3A%22RARB.seg3%22%2C%22refName%22%3A%22der3_RARB_BICC1_TRHDE%22%2C%22start%22%3A33126%2C%22end%22%3A39549%2C%22strand%22%3A-1%2C%22type%22%3A%22gene%22%2C%22name%22%3A%22RARB%22%2C%22subfeatures%22%3A%5B%7B%22uniqueId%22%3A%22NM_001290216.3.seg3%22%2C%22refName%22%3A%22der3_RARB_BICC1_TRHDE%22%2C%22start%22%3A33126%2C%22end%22%3A39549%2C%22strand%22%3A-1%2C%22type%22%3A%22transcript%22%2C%22name%22%3A%22NM_001290216.3%22%7D%5D%7D%5D%7D%7D%2C%7B%22type%22%3A%22VariantTrack%22%2C%22trackId%22%3A%22COLO829_truth_set%22%2C%22name%22%3A%22COLO829+validated+somatic+SVs+%28Valle-Incl%C3%A1n+2022%29%22%2C%22assemblyNames%22%3A%5B%22hg38%22%5D%2C%22adapter%22%3A%7B%22type%22%3A%22VcfAdapter%22%2C%22vcfLocation%22%3A%7B%22uri%22%3A%22https%3A%2F%2Fzenodo.org%2Fapi%2Frecords%2F4716169%2Ffiles%2Ftruthset_somaticSVs_COLO829_hg38lifted.vcf%2Fcontent%22%7D%7D%7D%5D%2C%22views%22%3A%5B%7B%22type%22%3A%22LinearSyntenyView%22%2C%22displayName%22%3A%22Two+templated+inserts+join+the+chr3+arms%22%2C%22views%22%3A%5B%7B%22assembly%22%3A%22hg38%22%2C%22loc%22%3A%22chr3%3A25358500-25360100+chr10%3A58717200-58717920+chr12%3A72272880-72273520%22%2C%22tracks%22%3A%5B%7B%22trackId%22%3A%22ncbi_refseq_hg38%22%2C%22geneGlyphMode%22%3A%22longestCoding%22%2C%22height%22%3A55%2C%22displayMode%22%3A%22compact%22%7D%2C%7B%22trackId%22%3A%22COLO829_truth_set%22%2C%22displayMode%22%3A%22collapsed%22%2C%22height%22%3A30%7D%2C%7B%22trackId%22%3A%22COLO829_tumor_ont%22%2C%22type%22%3A%22LinearAlignmentsDisplay%22%2C%22forceLoad%22%3Atrue%2C%22filterBy%22%3A%7B%22split%22%3A%22only%22%7D%2C%22linkedReads%22%3A%22normal%22%2C%22showBezierConnections%22%3Atrue%2C%22heightMode%22%3A%22grow%22%2C%22height%22%3A170%2C%22featureHeight%22%3A5%2C%22flipStrandLongReadChains%22%3Afalse%2C%22showLegend%22%3Atrue%2C%22showCoverage%22%3Atrue%2C%22coverageHeight%22%3A40%2C%22readConnections%22%3A%22arc%22%7D%5D%7D%2C%7B%22assembly%22%3A%22der3_RARB_BICC1_TRHDE%22%2C%22loc%22%3A%22der3_RARB_BICC1_TRHDE%3A32%2C300-33%2C400%22%2C%22showAminoAcids%22%3Afalse%2C%22tracks%22%3A%5B%22der3_segments%22%2C%7B%22trackId%22%3A%22der3_genes%22%2C%22geneGlyphMode%22%3A%22longestCoding%22%2C%22height%22%3A95%2C%22displayMode%22%3A%22compact%22%7D%2C%7B%22trackId%22%3A%22reads_vs_der3%22%2C%22type%22%3A%22LinearAlignmentsDisplay%22%2C%22heightMode%22%3A%22grow%22%2C%22height%22%3A175%2C%22featureHeight%22%3A5%2C%22flipStrandLongReadChains%22%3Afalse%2C%22coverageHeight%22%3A40%2C%22linkedReads%22%3A%22normal%22%2C%22filterBy%22%3A%7B%22flagInclude%22%3A0%2C%22flagExclude%22%3A1796%7D%7D%5D%7D%5D%2C%22tracks%22%3A%5B%5B%22der3_vs_hg38%22%5D%5D%2C%22drawCurves%22%3Atrue%2C%22levelHeights%22%3A%5B140%5D%7D%5D%7D&sessionName=JBrowse+docs%3A+cancer_sv%2Fderivative_inserts

A figure adds its tracks to one session. The jbrowse CLI writes the same tracks into a config.json instead, where every session that opens it has them: add-track where flags cover the whole track, add-track-json where they do not.

jbrowse add-track-json '{
  "type": "FeatureTrack",
  "trackId": "der3_genes",
  "name": "Reference genes projected onto the derivative",
  "assemblyNames": [
    "der3_RARB_BICC1_TRHDE"
  ],
  "adapter": {
    "type": "FromConfigAdapter",
    "features": [
      {
        "uniqueId": "RARB.seg0",
        "refName": "der3_RARB_BICC1_TRHDE",
        "start": 0,
        "end": 32732,
        "strand": 1,
        "type": "gene",
        "name": "RARB",
        "subfeatures": [
          {
            "uniqueId": "NM_001290216.3.seg0",
            "refName": "der3_RARB_BICC1_TRHDE",
            "start": 0,
            "end": 32732,
            "strand": 1,
            "type": "transcript",
            "name": "NM_001290216.3"
          },
          {
            "uniqueId": "NM_001290300.2.seg0",
            "refName": "der3_RARB_BICC1_TRHDE",
            "start": 13980,
            "end": 32732,
            "strand": 1,
            "type": "transcript",
            "name": "NM_001290300.2",
            "subfeatures": [
              {
                "uniqueId": "exon:NM_001290300.2.1.seg0",
                "refName": "der3_RARB_BICC1_TRHDE",
                "start": 13980,
                "end": 14070,
                "strand": 1,
                "type": "exon"
              },
              {
                "uniqueId": "CDS:NM_001290300.2.1.seg0",
                "refName": "der3_RARB_BICC1_TRHDE",
                "start": 14042,
                "end": 14070,
                "strand": 1,
                "type": "CDS"
              },
              {
                "uniqueId": "start_codon:NM_001290300.2.1.seg0",
                "refName": "der3_RARB_BICC1_TRHDE",
                "start": 14042,
                "end": 14045,
                "strand": 1,
                "type": "start_codon"
              }
            ]
          }
        ]
      },
      {
        "uniqueId": "LOC124906342.seg0",
        "refName": "der3_RARB_BICC1_TRHDE",
        "start": 9171,
        "end": 9237,
        "strand": 1,
        "type": "gene",
        "name": "LOC124906342",
        "subfeatures": [
          {
            "uniqueId": "XR_007096298.1.seg0",
            "refName": "der3_RARB_BICC1_TRHDE",
            "start": 9171,
            "end": 9237,
            "strand": 1,
            "type": "transcript",
            "name": "XR_007096298.1",
            "subfeatures": [
              {
                "uniqueId": "exon:XR_007096298.1.1.seg0",
                "refName": "der3_RARB_BICC1_TRHDE",
                "start": 9171,
                "end": 9237,
                "strand": 1,
                "type": "exon"
              }
            ]
          }
        ]
      },
      {
        "uniqueId": "BICC1.seg1",
        "refName": "der3_RARB_BICC1_TRHDE",
        "start": 32732,
        "end": 32931,
        "strand": 1,
        "type": "gene",
        "name": "BICC1",
        "subfeatures": [
          {
            "uniqueId": "XM_047425780.1.seg1",
            "refName": "der3_RARB_BICC1_TRHDE",
            "start": 32732,
            "end": 32931,
            "strand": 1,
            "type": "transcript",
            "name": "XM_047425780.1"
          }
        ]
      },
      {
        "uniqueId": "FAM133CP.seg1",
        "refName": "der3_RARB_BICC1_TRHDE",
        "start": 32732,
        "end": 32803,
        "strand": 1,
        "type": "gene",
        "name": "FAM133CP",
        "subfeatures": [
          {
            "uniqueId": "NR_027508.1.seg1",
            "refName": "der3_RARB_BICC1_TRHDE",
            "start": 32732,
            "end": 32803,
            "strand": 1,
            "type": "transcript",
            "name": "NR_027508.1",
            "subfeatures": [
              {
                "uniqueId": "exon:NR_027508.1.1.seg1",
                "refName": "der3_RARB_BICC1_TRHDE",
                "start": 32732,
                "end": 32803,
                "strand": 1,
                "type": "exon"
              }
            ]
          }
        ]
      },
      {
        "uniqueId": "TRHDE.seg2",
        "refName": "der3_RARB_BICC1_TRHDE",
        "start": 32932,
        "end": 33115,
        "strand": -1,
        "type": "gene",
        "name": "TRHDE",
        "subfeatures": [
          {
            "uniqueId": "XM_017019244.2.seg2",
            "refName": "der3_RARB_BICC1_TRHDE",
            "start": 32932,
            "end": 33115,
            "strand": -1,
            "type": "transcript",
            "name": "XM_017019244.2"
          },
          {
            "uniqueId": "XM_005268819.6.seg2",
            "refName": "der3_RARB_BICC1_TRHDE",
            "start": 32932,
            "end": 33115,
            "strand": -1,
            "type": "transcript",
            "name": "XM_005268819.6",
            "subfeatures": [
              {
                "uniqueId": "exon:XM_005268819.6.1.seg2",
                "refName": "der3_RARB_BICC1_TRHDE",
                "start": 32932,
                "end": 33115,
                "strand": -1,
                "type": "exon"
              },
              {
                "uniqueId": "CDS:XM_005268819.6.1.seg2",
                "refName": "der3_RARB_BICC1_TRHDE",
                "start": 32932,
                "end": 33115,
                "strand": -1,
                "type": "CDS"
              }
            ]
          }
        ]
      },
      {
        "uniqueId": "TRHDE-AS1.seg2",
        "refName": "der3_RARB_BICC1_TRHDE",
        "start": 32932,
        "end": 33115,
        "strand": 1,
        "type": "gene",
        "name": "TRHDE-AS1",
        "subfeatures": [
          {
            "uniqueId": "NR_026837.1.seg2",
            "refName": "der3_RARB_BICC1_TRHDE",
            "start": 32932,
            "end": 33115,
            "strand": 1,
            "type": "transcript",
            "name": "NR_026837.1",
            "subfeatures": [
              {
                "uniqueId": "exon:NR_026837.1.1.seg2",
                "refName": "der3_RARB_BICC1_TRHDE",
                "start": 32932,
                "end": 33115,
                "strand": 1,
                "type": "exon"
              }
            ]
          }
        ]
      },
      {
        "uniqueId": "RARB.seg3",
        "refName": "der3_RARB_BICC1_TRHDE",
        "start": 33126,
        "end": 39549,
        "strand": -1,
        "type": "gene",
        "name": "RARB",
        "subfeatures": [
          {
            "uniqueId": "NM_001290216.3.seg3",
            "refName": "der3_RARB_BICC1_TRHDE",
            "start": 33126,
            "end": 39549,
            "strand": -1,
            "type": "transcript",
            "name": "NM_001290216.3"
          }
        ]
      }
    ]
  }
}'

jbrowse add-track-json '{
  "type": "VariantTrack",
  "trackId": "COLO829_truth_set",
  "name": "COLO829 validated somatic SVs (Valle-Inclán 2022)",
  "assemblyNames": [
    "hg38"
  ],
  "adapter": {
    "type": "VcfAdapter",
    "vcfLocation": {
      "uri": "https://zenodo.org/api/records/4716169/files/truthset_somaticSVs_COLO829_hg38lifted.vcf/content"
    }
  }
}'

Run these where the config.json is, or add --out <dir>, and point each uri at your own file. The config needs der3_RARB_BICC1_TRHDE, hg38 already — jbrowse add-assembly adds yours. The location and the settings the steps carry are session state rather than track config — that half is the Session spec tab, or jbrowse set-default-session.

This session spec pastes after &session=spec- on any JBrowse Web instance.

{
  "sessionTracks": [
    {
      "type": "FeatureTrack",
      "trackId": "der3_genes",
      "name": "Reference genes projected onto the derivative",
      "assemblyNames": [
        "der3_RARB_BICC1_TRHDE"
      ],
      "adapter": {
        "type": "FromConfigAdapter",
        "features": [
          {
            "uniqueId": "RARB.seg0",
            "refName": "der3_RARB_BICC1_TRHDE",
            "start": 0,
            "end": 32732,
            "strand": 1,
            "type": "gene",
            "name": "RARB",
            "subfeatures": [
              {
                "uniqueId": "NM_001290216.3.seg0",
                "refName": "der3_RARB_BICC1_TRHDE",
                "start": 0,
                "end": 32732,
                "strand": 1,
                "type": "transcript",
                "name": "NM_001290216.3"
              },
              {
                "uniqueId": "NM_001290300.2.seg0",
                "refName": "der3_RARB_BICC1_TRHDE",
                "start": 13980,
                "end": 32732,
                "strand": 1,
                "type": "transcript",
                "name": "NM_001290300.2",
                "subfeatures": [
                  {
                    "uniqueId": "exon:NM_001290300.2.1.seg0",
                    "refName": "der3_RARB_BICC1_TRHDE",
                    "start": 13980,
                    "end": 14070,
                    "strand": 1,
                    "type": "exon"
                  },
                  {
                    "uniqueId": "CDS:NM_001290300.2.1.seg0",
                    "refName": "der3_RARB_BICC1_TRHDE",
                    "start": 14042,
                    "end": 14070,
                    "strand": 1,
                    "type": "CDS"
                  },
                  {
                    "uniqueId": "start_codon:NM_001290300.2.1.seg0",
                    "refName": "der3_RARB_BICC1_TRHDE",
                    "start": 14042,
                    "end": 14045,
                    "strand": 1,
                    "type": "start_codon"
                  }
                ]
              }
            ]
          },
          {
            "uniqueId": "LOC124906342.seg0",
            "refName": "der3_RARB_BICC1_TRHDE",
            "start": 9171,
            "end": 9237,
            "strand": 1,
            "type": "gene",
            "name": "LOC124906342",
            "subfeatures": [
              {
                "uniqueId": "XR_007096298.1.seg0",
                "refName": "der3_RARB_BICC1_TRHDE",
                "start": 9171,
                "end": 9237,
                "strand": 1,
                "type": "transcript",
                "name": "XR_007096298.1",
                "subfeatures": [
                  {
                    "uniqueId": "exon:XR_007096298.1.1.seg0",
                    "refName": "der3_RARB_BICC1_TRHDE",
                    "start": 9171,
                    "end": 9237,
                    "strand": 1,
                    "type": "exon"
                  }
                ]
              }
            ]
          },
          {
            "uniqueId": "BICC1.seg1",
            "refName": "der3_RARB_BICC1_TRHDE",
            "start": 32732,
            "end": 32931,
            "strand": 1,
            "type": "gene",
            "name": "BICC1",
            "subfeatures": [
              {
                "uniqueId": "XM_047425780.1.seg1",
                "refName": "der3_RARB_BICC1_TRHDE",
                "start": 32732,
                "end": 32931,
                "strand": 1,
                "type": "transcript",
                "name": "XM_047425780.1"
              }
            ]
          },
          {
            "uniqueId": "FAM133CP.seg1",
            "refName": "der3_RARB_BICC1_TRHDE",
            "start": 32732,
            "end": 32803,
            "strand": 1,
            "type": "gene",
            "name": "FAM133CP",
            "subfeatures": [
              {
                "uniqueId": "NR_027508.1.seg1",
                "refName": "der3_RARB_BICC1_TRHDE",
                "start": 32732,
                "end": 32803,
                "strand": 1,
                "type": "transcript",
                "name": "NR_027508.1",
                "subfeatures": [
                  {
                    "uniqueId": "exon:NR_027508.1.1.seg1",
                    "refName": "der3_RARB_BICC1_TRHDE",
                    "start": 32732,
                    "end": 32803,
                    "strand": 1,
                    "type": "exon"
                  }
                ]
              }
            ]
          },
          {
            "uniqueId": "TRHDE.seg2",
            "refName": "der3_RARB_BICC1_TRHDE",
            "start": 32932,
            "end": 33115,
            "strand": -1,
            "type": "gene",
            "name": "TRHDE",
            "subfeatures": [
              {
                "uniqueId": "XM_017019244.2.seg2",
                "refName": "der3_RARB_BICC1_TRHDE",
                "start": 32932,
                "end": 33115,
                "strand": -1,
                "type": "transcript",
                "name": "XM_017019244.2"
              },
              {
                "uniqueId": "XM_005268819.6.seg2",
                "refName": "der3_RARB_BICC1_TRHDE",
                "start": 32932,
                "end": 33115,
                "strand": -1,
                "type": "transcript",
                "name": "XM_005268819.6",
                "subfeatures": [
                  {
                    "uniqueId": "exon:XM_005268819.6.1.seg2",
                    "refName": "der3_RARB_BICC1_TRHDE",
                    "start": 32932,
                    "end": 33115,
                    "strand": -1,
                    "type": "exon"
                  },
                  {
                    "uniqueId": "CDS:XM_005268819.6.1.seg2",
                    "refName": "der3_RARB_BICC1_TRHDE",
                    "start": 32932,
                    "end": 33115,
                    "strand": -1,
                    "type": "CDS"
                  }
                ]
              }
            ]
          },
          {
            "uniqueId": "TRHDE-AS1.seg2",
            "refName": "der3_RARB_BICC1_TRHDE",
            "start": 32932,
            "end": 33115,
            "strand": 1,
            "type": "gene",
            "name": "TRHDE-AS1",
            "subfeatures": [
              {
                "uniqueId": "NR_026837.1.seg2",
                "refName": "der3_RARB_BICC1_TRHDE",
                "start": 32932,
                "end": 33115,
                "strand": 1,
                "type": "transcript",
                "name": "NR_026837.1",
                "subfeatures": [
                  {
                    "uniqueId": "exon:NR_026837.1.1.seg2",
                    "refName": "der3_RARB_BICC1_TRHDE",
                    "start": 32932,
                    "end": 33115,
                    "strand": 1,
                    "type": "exon"
                  }
                ]
              }
            ]
          },
          {
            "uniqueId": "RARB.seg3",
            "refName": "der3_RARB_BICC1_TRHDE",
            "start": 33126,
            "end": 39549,
            "strand": -1,
            "type": "gene",
            "name": "RARB",
            "subfeatures": [
              {
                "uniqueId": "NM_001290216.3.seg3",
                "refName": "der3_RARB_BICC1_TRHDE",
                "start": 33126,
                "end": 39549,
                "strand": -1,
                "type": "transcript",
                "name": "NM_001290216.3"
              }
            ]
          }
        ]
      }
    },
    {
      "type": "VariantTrack",
      "trackId": "COLO829_truth_set",
      "name": "COLO829 validated somatic SVs (Valle-Inclán 2022)",
      "assemblyNames": [
        "hg38"
      ],
      "adapter": {
        "type": "VcfAdapter",
        "vcfLocation": {
          "uri": "https://zenodo.org/api/records/4716169/files/truthset_somaticSVs_COLO829_hg38lifted.vcf/content"
        }
      }
    }
  ],
  "views": [
    {
      "type": "LinearSyntenyView",
      "displayName": "Two templated inserts join the chr3 arms",
      "views": [
        {
          "assembly": "hg38",
          "loc": "chr3:25358500-25360100 chr10:58717200-58717920 chr12:72272880-72273520",
          "tracks": [
            {
              "trackId": "ncbi_refseq_hg38",
              "geneGlyphMode": "longestCoding",
              "height": 55,
              "displayMode": "compact"
            },
            {
              "trackId": "COLO829_truth_set",
              "displayMode": "collapsed",
              "height": 30
            },
            {
              "trackId": "COLO829_tumor_ont",
              "type": "LinearAlignmentsDisplay",
              "forceLoad": true,
              "filterBy": {
                "split": "only"
              },
              "linkedReads": "normal",
              "showBezierConnections": true,
              "heightMode": "grow",
              "height": 170,
              "featureHeight": 5,
              "flipStrandLongReadChains": false,
              "showLegend": true,
              "showCoverage": true,
              "coverageHeight": 40,
              "readConnections": "arc"
            }
          ]
        },
        {
          "assembly": "der3_RARB_BICC1_TRHDE",
          "loc": "der3_RARB_BICC1_TRHDE:32,300-33,400",
          "showAminoAcids": false,
          "tracks": [
            "der3_segments",
            {
              "trackId": "der3_genes",
              "geneGlyphMode": "longestCoding",
              "height": 95,
              "displayMode": "compact"
            },
            {
              "trackId": "reads_vs_der3",
              "type": "LinearAlignmentsDisplay",
              "heightMode": "grow",
              "height": 175,
              "featureHeight": 5,
              "flipStrandLongReadChains": false,
              "coverageHeight": 40,
              "linkedReads": "normal",
              "filterBy": {
                "flagInclude": 0,
                "flagExclude": 1796
              }
            }
          ]
        }
      ],
      "tracks": [
        [
          "der3_vs_hg38"
        ]
      ],
      "drawCurves": true,
      "levelHeights": [
        140
      ]
    }
  ]
}

Loaded against config: https://jbrowse.org/demos/cancer_sv/config.json

The same view with jbrowse-anywidget, from the config the figure loads. Swap a track's uri for your own file.

from jbrowse_anywidget import JBrowseApp, fetch_hub

config = fetch_hub("https://jbrowse.org/demos/cancer_sv/config.json")
app = JBrowseApp(
    assemblies=config["assemblies"],
    tracks=config.get("tracks", []) + [
        {
            "type": "FeatureTrack",
            "trackId": "der3_genes",
            "name": "Reference genes projected onto the derivative",
            "assemblyNames": [
                "der3_RARB_BICC1_TRHDE"
            ],
            "adapter": {
                "type": "FromConfigAdapter",
                "features": [
                    {
                        "uniqueId": "RARB.seg0",
                        "refName": "der3_RARB_BICC1_TRHDE",
                        "start": 0,
                        "end": 32732,
                        "strand": 1,
                        "type": "gene",
                        "name": "RARB",
                        "subfeatures": [
                            {
                                "uniqueId": "NM_001290216.3.seg0",
                                "refName": "der3_RARB_BICC1_TRHDE",
                                "start": 0,
                                "end": 32732,
                                "strand": 1,
                                "type": "transcript",
                                "name": "NM_001290216.3"
                            },
                            {
                                "uniqueId": "NM_001290300.2.seg0",
                                "refName": "der3_RARB_BICC1_TRHDE",
                                "start": 13980,
                                "end": 32732,
                                "strand": 1,
                                "type": "transcript",
                                "name": "NM_001290300.2",
                                "subfeatures": [
                                    {
                                        "uniqueId": "exon:NM_001290300.2.1.seg0",
                                        "refName": "der3_RARB_BICC1_TRHDE",
                                        "start": 13980,
                                        "end": 14070,
                                        "strand": 1,
                                        "type": "exon"
                                    },
                                    {
                                        "uniqueId": "CDS:NM_001290300.2.1.seg0",
                                        "refName": "der3_RARB_BICC1_TRHDE",
                                        "start": 14042,
                                        "end": 14070,
                                        "strand": 1,
                                        "type": "CDS"
                                    },
                                    {
                                        "uniqueId": "start_codon:NM_001290300.2.1.seg0",
                                        "refName": "der3_RARB_BICC1_TRHDE",
                                        "start": 14042,
                                        "end": 14045,
                                        "strand": 1,
                                        "type": "start_codon"
                                    }
                                ]
                            }
                        ]
                    },
                    {
                        "uniqueId": "LOC124906342.seg0",
                        "refName": "der3_RARB_BICC1_TRHDE",
                        "start": 9171,
                        "end": 9237,
                        "strand": 1,
                        "type": "gene",
                        "name": "LOC124906342",
                        "subfeatures": [
                            {
                                "uniqueId": "XR_007096298.1.seg0",
                                "refName": "der3_RARB_BICC1_TRHDE",
                                "start": 9171,
                                "end": 9237,
                                "strand": 1,
                                "type": "transcript",
                                "name": "XR_007096298.1",
                                "subfeatures": [
                                    {
                                        "uniqueId": "exon:XR_007096298.1.1.seg0",
                                        "refName": "der3_RARB_BICC1_TRHDE",
                                        "start": 9171,
                                        "end": 9237,
                                        "strand": 1,
                                        "type": "exon"
                                    }
                                ]
                            }
                        ]
                    },
                    {
                        "uniqueId": "BICC1.seg1",
                        "refName": "der3_RARB_BICC1_TRHDE",
                        "start": 32732,
                        "end": 32931,
                        "strand": 1,
                        "type": "gene",
                        "name": "BICC1",
                        "subfeatures": [
                            {
                                "uniqueId": "XM_047425780.1.seg1",
                                "refName": "der3_RARB_BICC1_TRHDE",
                                "start": 32732,
                                "end": 32931,
                                "strand": 1,
                                "type": "transcript",
                                "name": "XM_047425780.1"
                            }
                        ]
                    },
                    {
                        "uniqueId": "FAM133CP.seg1",
                        "refName": "der3_RARB_BICC1_TRHDE",
                        "start": 32732,
                        "end": 32803,
                        "strand": 1,
                        "type": "gene",
                        "name": "FAM133CP",
                        "subfeatures": [
                            {
                                "uniqueId": "NR_027508.1.seg1",
                                "refName": "der3_RARB_BICC1_TRHDE",
                                "start": 32732,
                                "end": 32803,
                                "strand": 1,
                                "type": "transcript",
                                "name": "NR_027508.1",
                                "subfeatures": [
                                    {
                                        "uniqueId": "exon:NR_027508.1.1.seg1",
                                        "refName": "der3_RARB_BICC1_TRHDE",
                                        "start": 32732,
                                        "end": 32803,
                                        "strand": 1,
                                        "type": "exon"
                                    }
                                ]
                            }
                        ]
                    },
                    {
                        "uniqueId": "TRHDE.seg2",
                        "refName": "der3_RARB_BICC1_TRHDE",
                        "start": 32932,
                        "end": 33115,
                        "strand": -1,
                        "type": "gene",
                        "name": "TRHDE",
                        "subfeatures": [
                            {
                                "uniqueId": "XM_017019244.2.seg2",
                                "refName": "der3_RARB_BICC1_TRHDE",
                                "start": 32932,
                                "end": 33115,
                                "strand": -1,
                                "type": "transcript",
                                "name": "XM_017019244.2"
                            },
                            {
                                "uniqueId": "XM_005268819.6.seg2",
                                "refName": "der3_RARB_BICC1_TRHDE",
                                "start": 32932,
                                "end": 33115,
                                "strand": -1,
                                "type": "transcript",
                                "name": "XM_005268819.6",
                                "subfeatures": [
                                    {
                                        "uniqueId": "exon:XM_005268819.6.1.seg2",
                                        "refName": "der3_RARB_BICC1_TRHDE",
                                        "start": 32932,
                                        "end": 33115,
                                        "strand": -1,
                                        "type": "exon"
                                    },
                                    {
                                        "uniqueId": "CDS:XM_005268819.6.1.seg2",
                                        "refName": "der3_RARB_BICC1_TRHDE",
                                        "start": 32932,
                                        "end": 33115,
                                        "strand": -1,
                                        "type": "CDS"
                                    }
                                ]
                            }
                        ]
                    },
                    {
                        "uniqueId": "TRHDE-AS1.seg2",
                        "refName": "der3_RARB_BICC1_TRHDE",
                        "start": 32932,
                        "end": 33115,
                        "strand": 1,
                        "type": "gene",
                        "name": "TRHDE-AS1",
                        "subfeatures": [
                            {
                                "uniqueId": "NR_026837.1.seg2",
                                "refName": "der3_RARB_BICC1_TRHDE",
                                "start": 32932,
                                "end": 33115,
                                "strand": 1,
                                "type": "transcript",
                                "name": "NR_026837.1",
                                "subfeatures": [
                                    {
                                        "uniqueId": "exon:NR_026837.1.1.seg2",
                                        "refName": "der3_RARB_BICC1_TRHDE",
                                        "start": 32932,
                                        "end": 33115,
                                        "strand": 1,
                                        "type": "exon"
                                    }
                                ]
                            }
                        ]
                    },
                    {
                        "uniqueId": "RARB.seg3",
                        "refName": "der3_RARB_BICC1_TRHDE",
                        "start": 33126,
                        "end": 39549,
                        "strand": -1,
                        "type": "gene",
                        "name": "RARB",
                        "subfeatures": [
                            {
                                "uniqueId": "NM_001290216.3.seg3",
                                "refName": "der3_RARB_BICC1_TRHDE",
                                "start": 33126,
                                "end": 39549,
                                "strand": -1,
                                "type": "transcript",
                                "name": "NM_001290216.3"
                            }
                        ]
                    }
                ]
            }
        },
        {
            "type": "VariantTrack",
            "trackId": "COLO829_truth_set",
            "name": "COLO829 validated somatic SVs (Valle-Inclán 2022)",
            "assemblyNames": [
                "hg38"
            ],
            "adapter": {
                "type": "VcfAdapter",
                "vcfLocation": {
                    "uri": "https://zenodo.org/api/records/4716169/files/truthset_somaticSVs_COLO829_hg38lifted.vcf/content"
                }
            }
        }
    ],
    views=[
        {
            "type": "LinearSyntenyView",
            "displayName": "Two templated inserts join the chr3 arms",
            "views": [
                {
                    "assembly": "hg38",
                    "loc": "chr3:25358500-25360100 chr10:58717200-58717920 chr12:72272880-72273520",
                    "tracks": [
                        {
                            "trackId": "ncbi_refseq_hg38",
                            "geneGlyphMode": "longestCoding",
                            "height": 55,
                            "displayMode": "compact"
                        },
                        {
                            "trackId": "COLO829_truth_set",
                            "displayMode": "collapsed",
                            "height": 30
                        },
                        {
                            "trackId": "COLO829_tumor_ont",
                            "type": "LinearAlignmentsDisplay",
                            "forceLoad": True,
                            "filterBy": {
                                "split": "only"
                            },
                            "linkedReads": "normal",
                            "showBezierConnections": True,
                            "heightMode": "grow",
                            "height": 170,
                            "featureHeight": 5,
                            "flipStrandLongReadChains": False,
                            "showLegend": True,
                            "showCoverage": True,
                            "coverageHeight": 40,
                            "readConnections": "arc"
                        }
                    ]
                },
                {
                    "assembly": "der3_RARB_BICC1_TRHDE",
                    "loc": "der3_RARB_BICC1_TRHDE:32,300-33,400",
                    "showAminoAcids": False,
                    "tracks": [
                        "der3_segments",
                        {
                            "trackId": "der3_genes",
                            "geneGlyphMode": "longestCoding",
                            "height": 95,
                            "displayMode": "compact"
                        },
                        {
                            "trackId": "reads_vs_der3",
                            "type": "LinearAlignmentsDisplay",
                            "heightMode": "grow",
                            "height": 175,
                            "featureHeight": 5,
                            "flipStrandLongReadChains": False,
                            "coverageHeight": 40,
                            "linkedReads": "normal",
                            "filterBy": {
                                "flagInclude": 0,
                                "flagExclude": 1796
                            }
                        }
                    ]
                }
            ],
            "tracks": [
                [
                    "der3_vs_hg38"
                ]
            ],
            "drawCurves": True,
            "levelHeights": [
                140
            ]
        }
    ],
)
app  # display the widget

Hand this to a coding agent. It rebuilds the figure above headlessly, and the session file is then the thing to edit — swap an adapter uri for your own file and rerun.

cat > session.json <<'JSON'
{
  "sessionTracks": [
    {
      "type": "FeatureTrack",
      "trackId": "der3_genes",
      "name": "Reference genes projected onto the derivative",
      "assemblyNames": [
        "der3_RARB_BICC1_TRHDE"
      ],
      "adapter": {
        "type": "FromConfigAdapter",
        "features": [
          {
            "uniqueId": "RARB.seg0",
            "refName": "der3_RARB_BICC1_TRHDE",
            "start": 0,
            "end": 32732,
            "strand": 1,
            "type": "gene",
            "name": "RARB",
            "subfeatures": [
              {
                "uniqueId": "NM_001290216.3.seg0",
                "refName": "der3_RARB_BICC1_TRHDE",
                "start": 0,
                "end": 32732,
                "strand": 1,
                "type": "transcript",
                "name": "NM_001290216.3"
              },
              {
                "uniqueId": "NM_001290300.2.seg0",
                "refName": "der3_RARB_BICC1_TRHDE",
                "start": 13980,
                "end": 32732,
                "strand": 1,
                "type": "transcript",
                "name": "NM_001290300.2",
                "subfeatures": [
                  {
                    "uniqueId": "exon:NM_001290300.2.1.seg0",
                    "refName": "der3_RARB_BICC1_TRHDE",
                    "start": 13980,
                    "end": 14070,
                    "strand": 1,
                    "type": "exon"
                  },
                  {
                    "uniqueId": "CDS:NM_001290300.2.1.seg0",
                    "refName": "der3_RARB_BICC1_TRHDE",
                    "start": 14042,
                    "end": 14070,
                    "strand": 1,
                    "type": "CDS"
                  },
                  {
                    "uniqueId": "start_codon:NM_001290300.2.1.seg0",
                    "refName": "der3_RARB_BICC1_TRHDE",
                    "start": 14042,
                    "end": 14045,
                    "strand": 1,
                    "type": "start_codon"
                  }
                ]
              }
            ]
          },
          {
            "uniqueId": "LOC124906342.seg0",
            "refName": "der3_RARB_BICC1_TRHDE",
            "start": 9171,
            "end": 9237,
            "strand": 1,
            "type": "gene",
            "name": "LOC124906342",
            "subfeatures": [
              {
                "uniqueId": "XR_007096298.1.seg0",
                "refName": "der3_RARB_BICC1_TRHDE",
                "start": 9171,
                "end": 9237,
                "strand": 1,
                "type": "transcript",
                "name": "XR_007096298.1",
                "subfeatures": [
                  {
                    "uniqueId": "exon:XR_007096298.1.1.seg0",
                    "refName": "der3_RARB_BICC1_TRHDE",
                    "start": 9171,
                    "end": 9237,
                    "strand": 1,
                    "type": "exon"
                  }
                ]
              }
            ]
          },
          {
            "uniqueId": "BICC1.seg1",
            "refName": "der3_RARB_BICC1_TRHDE",
            "start": 32732,
            "end": 32931,
            "strand": 1,
            "type": "gene",
            "name": "BICC1",
            "subfeatures": [
              {
                "uniqueId": "XM_047425780.1.seg1",
                "refName": "der3_RARB_BICC1_TRHDE",
                "start": 32732,
                "end": 32931,
                "strand": 1,
                "type": "transcript",
                "name": "XM_047425780.1"
              }
            ]
          },
          {
            "uniqueId": "FAM133CP.seg1",
            "refName": "der3_RARB_BICC1_TRHDE",
            "start": 32732,
            "end": 32803,
            "strand": 1,
            "type": "gene",
            "name": "FAM133CP",
            "subfeatures": [
              {
                "uniqueId": "NR_027508.1.seg1",
                "refName": "der3_RARB_BICC1_TRHDE",
                "start": 32732,
                "end": 32803,
                "strand": 1,
                "type": "transcript",
                "name": "NR_027508.1",
                "subfeatures": [
                  {
                    "uniqueId": "exon:NR_027508.1.1.seg1",
                    "refName": "der3_RARB_BICC1_TRHDE",
                    "start": 32732,
                    "end": 32803,
                    "strand": 1,
                    "type": "exon"
                  }
                ]
              }
            ]
          },
          {
            "uniqueId": "TRHDE.seg2",
            "refName": "der3_RARB_BICC1_TRHDE",
            "start": 32932,
            "end": 33115,
            "strand": -1,
            "type": "gene",
            "name": "TRHDE",
            "subfeatures": [
              {
                "uniqueId": "XM_017019244.2.seg2",
                "refName": "der3_RARB_BICC1_TRHDE",
                "start": 32932,
                "end": 33115,
                "strand": -1,
                "type": "transcript",
                "name": "XM_017019244.2"
              },
              {
                "uniqueId": "XM_005268819.6.seg2",
                "refName": "der3_RARB_BICC1_TRHDE",
                "start": 32932,
                "end": 33115,
                "strand": -1,
                "type": "transcript",
                "name": "XM_005268819.6",
                "subfeatures": [
                  {
                    "uniqueId": "exon:XM_005268819.6.1.seg2",
                    "refName": "der3_RARB_BICC1_TRHDE",
                    "start": 32932,
                    "end": 33115,
                    "strand": -1,
                    "type": "exon"
                  },
                  {
                    "uniqueId": "CDS:XM_005268819.6.1.seg2",
                    "refName": "der3_RARB_BICC1_TRHDE",
                    "start": 32932,
                    "end": 33115,
                    "strand": -1,
                    "type": "CDS"
                  }
                ]
              }
            ]
          },
          {
            "uniqueId": "TRHDE-AS1.seg2",
            "refName": "der3_RARB_BICC1_TRHDE",
            "start": 32932,
            "end": 33115,
            "strand": 1,
            "type": "gene",
            "name": "TRHDE-AS1",
            "subfeatures": [
              {
                "uniqueId": "NR_026837.1.seg2",
                "refName": "der3_RARB_BICC1_TRHDE",
                "start": 32932,
                "end": 33115,
                "strand": 1,
                "type": "transcript",
                "name": "NR_026837.1",
                "subfeatures": [
                  {
                    "uniqueId": "exon:NR_026837.1.1.seg2",
                    "refName": "der3_RARB_BICC1_TRHDE",
                    "start": 32932,
                    "end": 33115,
                    "strand": 1,
                    "type": "exon"
                  }
                ]
              }
            ]
          },
          {
            "uniqueId": "RARB.seg3",
            "refName": "der3_RARB_BICC1_TRHDE",
            "start": 33126,
            "end": 39549,
            "strand": -1,
            "type": "gene",
            "name": "RARB",
            "subfeatures": [
              {
                "uniqueId": "NM_001290216.3.seg3",
                "refName": "der3_RARB_BICC1_TRHDE",
                "start": 33126,
                "end": 39549,
                "strand": -1,
                "type": "transcript",
                "name": "NM_001290216.3"
              }
            ]
          }
        ]
      }
    },
    {
      "type": "VariantTrack",
      "trackId": "COLO829_truth_set",
      "name": "COLO829 validated somatic SVs (Valle-Inclán 2022)",
      "assemblyNames": [
        "hg38"
      ],
      "adapter": {
        "type": "VcfAdapter",
        "vcfLocation": {
          "uri": "https://zenodo.org/api/records/4716169/files/truthset_somaticSVs_COLO829_hg38lifted.vcf/content"
        }
      }
    }
  ],
  "views": [
    {
      "type": "LinearSyntenyView",
      "displayName": "Two templated inserts join the chr3 arms",
      "views": [
        {
          "assembly": "hg38",
          "loc": "chr3:25358500-25360100 chr10:58717200-58717920 chr12:72272880-72273520",
          "tracks": [
            {
              "trackId": "ncbi_refseq_hg38",
              "geneGlyphMode": "longestCoding",
              "height": 55,
              "displayMode": "compact"
            },
            {
              "trackId": "COLO829_truth_set",
              "displayMode": "collapsed",
              "height": 30
            },
            {
              "trackId": "COLO829_tumor_ont",
              "type": "LinearAlignmentsDisplay",
              "forceLoad": true,
              "filterBy": {
                "split": "only"
              },
              "linkedReads": "normal",
              "showBezierConnections": true,
              "heightMode": "grow",
              "height": 170,
              "featureHeight": 5,
              "flipStrandLongReadChains": false,
              "showLegend": true,
              "showCoverage": true,
              "coverageHeight": 40,
              "readConnections": "arc"
            }
          ]
        },
        {
          "assembly": "der3_RARB_BICC1_TRHDE",
          "loc": "der3_RARB_BICC1_TRHDE:32,300-33,400",
          "showAminoAcids": false,
          "tracks": [
            "der3_segments",
            {
              "trackId": "der3_genes",
              "geneGlyphMode": "longestCoding",
              "height": 95,
              "displayMode": "compact"
            },
            {
              "trackId": "reads_vs_der3",
              "type": "LinearAlignmentsDisplay",
              "heightMode": "grow",
              "height": 175,
              "featureHeight": 5,
              "flipStrandLongReadChains": false,
              "coverageHeight": 40,
              "linkedReads": "normal",
              "filterBy": {
                "flagInclude": 0,
                "flagExclude": 1796
              }
            }
          ]
        }
      ],
      "tracks": [
        [
          "der3_vs_hg38"
        ]
      ],
      "drawCurves": true,
      "levelHeights": [
        140
      ]
    }
  ]
}
JSON

npx @jbrowse/capture --instance https://jbrowse.org/code/jb2/main/ \
  --config https://jbrowse.org/demos/cancer_sv/config.json \
  --session session.json -o figure.png

Using JBrowse with AI agents covers the rest: hosted genomes to point it at, and why waiting for the render is the part that goes wrong.

A breakpoint split view follows one read across its alignments: soft clipping is shown on both sides, and a curve joins each molecule's pieces. A dashed connector means the read passes through a segment no panel is showing.

COLO829 tumor ONT reads over one junction, twice. Against hg38 (left, split alignments only) they stop at chr3:25,359,568 with their tails clipped; realigned to the derivative (right) they cross at flat depth. The panes are at different zooms. Open in JBrowse: hg38 ↗ (large dataset — this session takes a while to load) · derivative ↗

The steps behind the figure above, run against your own data.

  1. Click the view's title in its header and enter "RARB (chr3) - BICC1 (chr10) - TRHDE (chr12)"
  2. Open your genome: on the JBrowse Desktop start screen click Open new genome (or Show all available genomes to pick a hosted one).This figure uses hg38.
  3. Add your own track: open this view's track selector, click + and choose Add track, then paste a URL or choose a local file.This figure uses the “COLO829_tumor_ont” track.
  4. Click Force load in the track's "Zoom in to see features or force load" message.Loads the region even past the byte-size limit, which can be slow.
  5. Track menu → Show... → Show soft clipping (checked)Reveals clipped bases — the signal that a read spans a breakpoint.
  6. Track menu → Filter by... → Split alignments → Only split alignmentsA read filter drops reads in the worker before layout, so it thins the coverage histogram along with the pileup.
  7. Track menu → Read height → Custom... → 2px
  8. Drag the bar at the bottom edge of the track to resize it.
  9. Type your region of interest into the location box and press Enter.This figure is at chr3:25,357,000-25,362,000.
  10. Open your genome: on the JBrowse Desktop start screen click Open new genome (or Show all available genomes to pick a hosted one).This figure uses hg38.
  11. Add your own track: open this view's track selector, click + and choose Add track, then paste a URL or choose a local file.This figure uses the “COLO829_tumor_ont” track.
  12. Click Force load in the track's "Zoom in to see features or force load" message.Loads the region even past the byte-size limit, which can be slow.
  13. Track menu → Show... → Show soft clipping (checked)Reveals clipped bases — the signal that a read spans a breakpoint.
  14. Track menu → Filter by... → Split alignments → Only split alignmentsA read filter drops reads in the worker before layout, so it thins the coverage histogram along with the pileup.
  15. Track menu → Read height → Custom... → 2px
  16. Drag the bar at the bottom edge of the track to resize it.
  17. Type your region of interest into the location box and press Enter.This figure is at chr10:58,715,000-58,720,000.
  18. Open your genome: on the JBrowse Desktop start screen click Open new genome (or Show all available genomes to pick a hosted one).This figure uses hg38.
  19. Add your own track: open this view's track selector, click + and choose Add track, then paste a URL or choose a local file.This figure uses the “COLO829_tumor_ont” track.
  20. Click Force load in the track's "Zoom in to see features or force load" message.Loads the region even past the byte-size limit, which can be slow.
  21. Track menu → Show... → Show soft clipping (checked)Reveals clipped bases — the signal that a read spans a breakpoint.
  22. Track menu → Filter by... → Split alignments → Only split alignmentsA read filter drops reads in the worker before layout, so it thins the coverage histogram along with the pileup.
  23. Track menu → Read height → Custom... → 2px
  24. Drag the bar at the bottom edge of the track to resize it.
  25. Type your region of interest into the location box and press Enter.This figure is at chr12:72,270,700-72,275,700.

Some settings have no written step yet — see the Session spec tab.

Open this view in JBrowse Desktop ↗

Opens JBrowse Desktop (JBrowse Desktop 5.0+) at this view and saves it as a reopenable session — swap in your own files afterwards.

Nothing happens? Paste this link into Desktop's Open JBrowse Web link... (start screen, or File → Session):

https://jbrowse.org/code/jb2/main/?config=https%3A%2F%2Fjbrowse.org%2Fdemos%2Fcancer_sv%2Fconfig.json&session=spec-%7B%22views%22%3A%5B%7B%22type%22%3A%22BreakpointSplitView%22%2C%22displayName%22%3A%22RARB+%28chr3%29+-+BICC1+%28chr10%29+-+TRHDE+%28chr12%29%22%2C%22height%22%3A800%2C%22views%22%3A%5B%7B%22assembly%22%3A%22hg38%22%2C%22loc%22%3A%22chr3%3A25%2C357%2C000-25%2C362%2C000%22%2C%22tracks%22%3A%5B%7B%22trackId%22%3A%22COLO829_tumor_ont%22%2C%22type%22%3A%22LinearAlignmentsDisplay%22%2C%22forceLoad%22%3Atrue%2C%22showSoftClipping%22%3Atrue%2C%22filterBy%22%3A%7B%22split%22%3A%22only%22%7D%2C%22featureHeight%22%3A2%2C%22height%22%3A280%7D%5D%7D%2C%7B%22assembly%22%3A%22hg38%22%2C%22loc%22%3A%22chr10%3A58%2C715%2C000-58%2C720%2C000%22%2C%22tracks%22%3A%5B%7B%22trackId%22%3A%22COLO829_tumor_ont%22%2C%22type%22%3A%22LinearAlignmentsDisplay%22%2C%22forceLoad%22%3Atrue%2C%22showSoftClipping%22%3Atrue%2C%22filterBy%22%3A%7B%22split%22%3A%22only%22%7D%2C%22featureHeight%22%3A2%2C%22height%22%3A150%7D%5D%7D%2C%7B%22assembly%22%3A%22hg38%22%2C%22loc%22%3A%22chr12%3A72%2C270%2C700-72%2C275%2C700%22%2C%22tracks%22%3A%5B%7B%22trackId%22%3A%22COLO829_tumor_ont%22%2C%22type%22%3A%22LinearAlignmentsDisplay%22%2C%22forceLoad%22%3Atrue%2C%22showSoftClipping%22%3Atrue%2C%22filterBy%22%3A%7B%22split%22%3A%22only%22%7D%2C%22featureHeight%22%3A2%2C%22height%22%3A150%7D%5D%7D%5D%7D%5D%7D&sessionName=JBrowse+docs%3A+cancer_sv%2Frealigned_reads_reference

This session spec pastes after &session=spec- on any JBrowse Web instance.

{
  "views": [
    {
      "type": "BreakpointSplitView",
      "displayName": "RARB (chr3) - BICC1 (chr10) - TRHDE (chr12)",
      "height": 800,
      "views": [
        {
          "assembly": "hg38",
          "loc": "chr3:25,357,000-25,362,000",
          "tracks": [
            {
              "trackId": "COLO829_tumor_ont",
              "type": "LinearAlignmentsDisplay",
              "forceLoad": true,
              "showSoftClipping": true,
              "filterBy": {
                "split": "only"
              },
              "featureHeight": 2,
              "height": 280
            }
          ]
        },
        {
          "assembly": "hg38",
          "loc": "chr10:58,715,000-58,720,000",
          "tracks": [
            {
              "trackId": "COLO829_tumor_ont",
              "type": "LinearAlignmentsDisplay",
              "forceLoad": true,
              "showSoftClipping": true,
              "filterBy": {
                "split": "only"
              },
              "featureHeight": 2,
              "height": 150
            }
          ]
        },
        {
          "assembly": "hg38",
          "loc": "chr12:72,270,700-72,275,700",
          "tracks": [
            {
              "trackId": "COLO829_tumor_ont",
              "type": "LinearAlignmentsDisplay",
              "forceLoad": true,
              "showSoftClipping": true,
              "filterBy": {
                "split": "only"
              },
              "featureHeight": 2,
              "height": 150
            }
          ]
        }
      ]
    }
  ]
}

Loaded against config: https://jbrowse.org/demos/cancer_sv/config.json

The same view with jbrowse-anywidget, from the config the figure loads. Swap a track's uri for your own file.

from jbrowse_anywidget import JBrowseApp, fetch_hub

config = fetch_hub("https://jbrowse.org/demos/cancer_sv/config.json")
app = JBrowseApp(
    assemblies=config["assemblies"],
    tracks=config.get("tracks", []),
    views=[
        {
            "type": "BreakpointSplitView",
            "displayName": "RARB (chr3) - BICC1 (chr10) - TRHDE (chr12)",
            "height": 800,
            "views": [
                {
                    "assembly": "hg38",
                    "loc": "chr3:25,357,000-25,362,000",
                    "tracks": [
                        {
                            "trackId": "COLO829_tumor_ont",
                            "type": "LinearAlignmentsDisplay",
                            "forceLoad": True,
                            "showSoftClipping": True,
                            "filterBy": {
                                "split": "only"
                            },
                            "featureHeight": 2,
                            "height": 280
                        }
                    ]
                },
                {
                    "assembly": "hg38",
                    "loc": "chr10:58,715,000-58,720,000",
                    "tracks": [
                        {
                            "trackId": "COLO829_tumor_ont",
                            "type": "LinearAlignmentsDisplay",
                            "forceLoad": True,
                            "showSoftClipping": True,
                            "filterBy": {
                                "split": "only"
                            },
                            "featureHeight": 2,
                            "height": 150
                        }
                    ]
                },
                {
                    "assembly": "hg38",
                    "loc": "chr12:72,270,700-72,275,700",
                    "tracks": [
                        {
                            "trackId": "COLO829_tumor_ont",
                            "type": "LinearAlignmentsDisplay",
                            "forceLoad": True,
                            "showSoftClipping": True,
                            "filterBy": {
                                "split": "only"
                            },
                            "featureHeight": 2,
                            "height": 150
                        }
                    ]
                }
            ]
        }
    ],
)
app  # display the widget

Hand this to a coding agent. It rebuilds the figure above headlessly, and the session file is then the thing to edit — swap an adapter uri for your own file and rerun.

cat > session.json <<'JSON'
{
  "views": [
    {
      "type": "BreakpointSplitView",
      "displayName": "RARB (chr3) - BICC1 (chr10) - TRHDE (chr12)",
      "height": 800,
      "views": [
        {
          "assembly": "hg38",
          "loc": "chr3:25,357,000-25,362,000",
          "tracks": [
            {
              "trackId": "COLO829_tumor_ont",
              "type": "LinearAlignmentsDisplay",
              "forceLoad": true,
              "showSoftClipping": true,
              "filterBy": {
                "split": "only"
              },
              "featureHeight": 2,
              "height": 280
            }
          ]
        },
        {
          "assembly": "hg38",
          "loc": "chr10:58,715,000-58,720,000",
          "tracks": [
            {
              "trackId": "COLO829_tumor_ont",
              "type": "LinearAlignmentsDisplay",
              "forceLoad": true,
              "showSoftClipping": true,
              "filterBy": {
                "split": "only"
              },
              "featureHeight": 2,
              "height": 150
            }
          ]
        },
        {
          "assembly": "hg38",
          "loc": "chr12:72,270,700-72,275,700",
          "tracks": [
            {
              "trackId": "COLO829_tumor_ont",
              "type": "LinearAlignmentsDisplay",
              "forceLoad": true,
              "showSoftClipping": true,
              "filterBy": {
                "split": "only"
              },
              "featureHeight": 2,
              "height": 150
            }
          ]
        }
      ]
    }
  ]
}
JSON

npx @jbrowse/capture --instance https://jbrowse.org/code/jb2/main/ \
  --config https://jbrowse.org/demos/cancer_sv/config.json \
  --session session.json -o figure.png

Using JBrowse with AI agents covers the rest: hosted genomes to point it at, and why waiting for the render is the part that goes wrong.

The steps behind the figure above, run against your own data.

  1. Open your genome: on the JBrowse Desktop start screen click Open new genome (or Show all available genomes to pick a hosted one).This figure uses der3_RARB_BICC1_TRHDE.
  2. Add your own track: File → Open track..., then paste a URL or choose a local file.This figure uses the “der3_segments” track.
  3. Drag the bar at the bottom edge of the track to resize it.“der3_segments”.
  4. Add your own track: File → Open track..., then paste a URL or choose a local file.This figure uses the “reads_vs_der3” track.
  5. Track menu → Show... → Show soft clipping (checked)Reveals clipped bases — the signal that a read spans a breakpoint.“reads_vs_der3”.
  6. Track menu → Read height → Custom... → 8px“reads_vs_der3”.
  7. Drag the bar at the bottom edge of the track to resize it.“reads_vs_der3”.
  8. Type your region of interest into the location box and press Enter.This figure is at der3_RARB_BICC1_TRHDE:32,545-32,925.
  9. View menu → Zoom to region / use the location box, then add a highlightThis figure highlights 1 region; highlights can also be set with the &highlight= URL parameter.

Open this view in JBrowse Desktop ↗

Opens JBrowse Desktop (JBrowse Desktop 5.0+) at this view and saves it as a reopenable session — swap in your own files afterwards.

Nothing happens? Paste this link into Desktop's Open JBrowse Web link... (start screen, or File → Session):

https://jbrowse.org/code/jb2/main/?config=https%3A%2F%2Fjbrowse.org%2Fdemos%2Fcancer_sv%2Fconfig.json&session=spec-%7B%22views%22%3A%5B%7B%22type%22%3A%22LinearGenomeView%22%2C%22assembly%22%3A%22der3_RARB_BICC1_TRHDE%22%2C%22loc%22%3A%22der3_RARB_BICC1_TRHDE%3A32%2C545-32%2C925%22%2C%22highlight%22%3A%5B%7B%22refName%22%3A%22der3_RARB_BICC1_TRHDE%22%2C%22start%22%3A32722%2C%22end%22%3A32742%2C%22color%22%3A%22rgba%2860%2C65%2C72%2C0.12%29%22%7D%5D%2C%22tracks%22%3A%5B%7B%22trackId%22%3A%22der3_segments%22%2C%22height%22%3A70%7D%2C%7B%22trackId%22%3A%22reads_vs_der3%22%2C%22type%22%3A%22LinearAlignmentsDisplay%22%2C%22showSoftClipping%22%3Atrue%2C%22featureHeight%22%3A8%2C%22height%22%3A470%7D%5D%7D%5D%7D&sessionName=JBrowse+docs%3A+cancer_sv%2Frealigned_reads_derivative

This session spec pastes after &session=spec- on any JBrowse Web instance.

{
  "views": [
    {
      "type": "LinearGenomeView",
      "assembly": "der3_RARB_BICC1_TRHDE",
      "loc": "der3_RARB_BICC1_TRHDE:32,545-32,925",
      "highlight": [
        {
          "refName": "der3_RARB_BICC1_TRHDE",
          "start": 32722,
          "end": 32742,
          "color": "rgba(60,65,72,0.12)"
        }
      ],
      "tracks": [
        {
          "trackId": "der3_segments",
          "height": 70
        },
        {
          "trackId": "reads_vs_der3",
          "type": "LinearAlignmentsDisplay",
          "showSoftClipping": true,
          "featureHeight": 8,
          "height": 470
        }
      ]
    }
  ]
}

Loaded against config: https://jbrowse.org/demos/cancer_sv/config.json

The same view with jbrowse-anywidget, from the config the figure loads. Swap a track's uri for your own file.

from jbrowse_anywidget import JBrowseApp, fetch_hub

config = fetch_hub("https://jbrowse.org/demos/cancer_sv/config.json")
app = JBrowseApp(
    assemblies=config["assemblies"],
    tracks=config.get("tracks", []),
    views=[
        {
            "type": "LinearGenomeView",
            "assembly": "der3_RARB_BICC1_TRHDE",
            "loc": "der3_RARB_BICC1_TRHDE:32,545-32,925",
            "highlight": [
                {
                    "refName": "der3_RARB_BICC1_TRHDE",
                    "start": 32722,
                    "end": 32742,
                    "color": "rgba(60,65,72,0.12)"
                }
            ],
            "tracks": [
                {
                    "trackId": "der3_segments",
                    "height": 70
                },
                {
                    "trackId": "reads_vs_der3",
                    "type": "LinearAlignmentsDisplay",
                    "showSoftClipping": True,
                    "featureHeight": 8,
                    "height": 470
                }
            ]
        }
    ],
)
app  # display the widget

Hand this to a coding agent. It rebuilds the figure above headlessly, and the session file is then the thing to edit — swap an adapter uri for your own file and rerun.

cat > session.json <<'JSON'
{
  "views": [
    {
      "type": "LinearGenomeView",
      "assembly": "der3_RARB_BICC1_TRHDE",
      "loc": "der3_RARB_BICC1_TRHDE:32,545-32,925",
      "highlight": [
        {
          "refName": "der3_RARB_BICC1_TRHDE",
          "start": 32722,
          "end": 32742,
          "color": "rgba(60,65,72,0.12)"
        }
      ],
      "tracks": [
        {
          "trackId": "der3_segments",
          "height": 70
        },
        {
          "trackId": "reads_vs_der3",
          "type": "LinearAlignmentsDisplay",
          "showSoftClipping": true,
          "featureHeight": 8,
          "height": 470
        }
      ]
    }
  ]
}
JSON

npx @jbrowse/capture --instance https://jbrowse.org/code/jb2/main/ \
  --config https://jbrowse.org/demos/cancer_sv/config.json \
  --session session.json -o figure.png

Using JBrowse with AI agents covers the rest: hosted genomes to point it at, and why waiting for the render is the part that goes wrong.

Reproduce it end to end

scripts/build_cancer_sv_demo.sh builds everything above from public sources:

curl -fO https://raw.githubusercontent.com/GMOD/jbrowse-components/main/scripts/build_cancer_sv_demo.sh
bash build_cancer_sv_demo.sh    # builds ./cancer_sv_build/jbrowse2
npx --yes serve cancer_sv_build/jbrowse2

The script fetches the ONT COLO829 somatic SV calls and coverage, and the published der(3) contig and its alignment. It builds the K562 half of the demo too, which Gene fusion calls and the DNA behind them walks through.

Every analysis step behind this page belongs to a tool built for it. JBrowse converts what they emit and shows it.

  • Calling somatic SVs and their complex clusters from long reads: Severus (Keskus et al. 2025) builds breakpoint graphs from phased tumor and normal reads and reports multi-break rearrangements as clusters. It was benchmarked on COLO829.
  • Ordering junctions into a derivative chromosome: LINX (Shale et al. 2022) chains breakends using allele-specific copy number from the Hartwig pipeline, and JaBbA with gGnome (Hadi et al. 2020) infers junction-balanced genome graphs whose walks are allelic paths. RCK (Aganezov and Raphael 2020) reconstructs haplotype-specific karyotypes under evolutionary constraints. All three take copy number.
  • Assembling the allele's sequence: a local de novo assembly of the reads pulled at the loci, with hifiasm, Flye or Shasta, and sawfish (Saunders et al. 2025) assembles SV haplotypes as part of calling on HiFi reads.
  • Drawing the figure: ReConPlot (Espejo Valle-Inclán and Cortés-Ciriano 2023) draws rearrangement and copy number plots for complex events in R, and Ribbon (Nattestad et al. 2021) draws one read's path across the reference, which the split view above follows.

See also

References