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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.13. Desktop beta builds are coming soon.

Cancer genomes have rearrangements that join several distant pieces of the genome into one molecule through a chain of junctions, each joining two distant stretches. We follow one such chain in the COLO829 melanoma cell line across the three chromosomes it visits, in a breakpoint split view, then align the derivative allele assembled from the reads that span it to the reference, in 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

All but the last file come from the ONT COLO829 open-data release and its wf-somatic-variation run; the last is the multi-platform truth set (Valle-Inclán et al. 2022).

The build script takes these files from their URLs, so there is nothing to download by hand.

COLO829 and its coverage tracks

The demo's tumor and normal coverage tracks are the wf-somatic-variation run's mosdepth output in 50 kb windows, converted to bigWig:

# awk keeps the contigs in hg38.chrom.sizes; bedGraphToBigWig fails on any other
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

The rearrangement chain across chr3, chr10 and chr12

A series of junctions can bring two genes together, as in the KLHDC2-SNTB1 fusion of the SK-BR-3 breast cancer line (Nattestad et al. 2018). The chain this page follows is COLO829's der(3), a derivative chromosome 3 assembled from pieces of three chromosomes, whose three junctions close a triangle across chr3, chr10 and chr12:

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 genes involved are RARB (a tumor suppressor) on chr3, BICC1 on chr10, and TRHDE on chr12.

Tumor and normal reads at the chr3 breakpoints

The ONT reads are aligned to GRCh38, so we load that assembly and the two read tracks. Each read file needs its index beside it, a .crai for the CRAM and a .bai for the BAM; for your own sample, swap the uri:

Goes in the assemblies array of config.json. See Assemblies.

{
  "name": "hg38",
  "uri": "https://jbrowse.org/genomes/GRCh38/fasta/hg38.prefix.fa.gz",
  "refNameAliases": {
    "uri": "https://s3.amazonaws.com/jbrowse.org/genomes/GRCh38/hg38_aliases.txt"
  },
  "cytobands": "https://jbrowse.org/genomes/GRCh38/cytoBand.txt"
}
jbrowse add-assembly https://jbrowse.org/genomes/GRCh38/fasta/hg38.prefix.fa.gz \
  --name hg38 \
  --refNameAliases https://s3.amazonaws.com/jbrowse.org/genomes/GRCh38/hg38_aliases.txt \
  --config '{"cytobands":"https://jbrowse.org/genomes/GRCh38/cytoBand.txt"}'

hg38 is one of the genomes JBrowse Desktop hosts, with gene tracks already set up: on the start screen click Show all available genomes and pick it. To load the files of this config instead:

In JBrowse Desktop, Open new genome on the start screen (or File → Open genome... in a session), then Open from a URL and paste, one per line:

https://jbrowse.org/genomes/GRCh38/fasta/hg38.prefix.fa.gz
https://jbrowse.org/genomes/GRCh38/fasta/hg38.prefix.fa.gz.fai
https://jbrowse.org/genomes/GRCh38/fasta/hg38.prefix.fa.gz.gzi

JBrowse reads the format off the file name. Then fill in:

  • Genome name: hg38
  • refName aliases (under More options): https://s3.amazonaws.com/jbrowse.org/genomes/GRCh38/hg38_aliases.txt
  • cytobands (under More options): https://jbrowse.org/genomes/GRCh38/cytoBand.txt

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

{
  "trackId": "COLO829_tumor_ont",
  "name": "COLO829 tumor (ONT R10)",
  "uri": "https://ont-open-data.s3.amazonaws.com/colo829_2024.03/wf_somatic_variation/sup/COLO829_tumor.ht.cram",
  "assemblyNames": ["hg38"]
}
jbrowse add-track https://ont-open-data.s3.amazonaws.com/colo829_2024.03/wf_somatic_variation/sup/COLO829_tumor.ht.cram \
  --trackId COLO829_tumor_ont \
  --name "COLO829 tumor (ONT R10)" \
  --assemblyNames hg38

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

  • Main file: https://ont-open-data.s3.amazonaws.com/colo829_2024.03/wf_somatic_variation/sup/COLO829_tumor.ht.cram

Click Next. JBrowse reads the adapter and track type off the file name. Then fill in:

  • Track name: COLO829 tumor (ONT R10)
  • Assembly: hg38

Click Add.

Open this track in JBrowse Web ↗

Open this track in JBrowse Desktop ↗ (JBrowse Desktop 5.0+)

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

{
  "trackId": "COLO829BL_normal_ont",
  "name": "COLO829BL matched normal (ONT R10)",
  "uri": "https://ont-open-data.s3.amazonaws.com/colo829_2024.03/basecalls/colo829bl/sup/PAU59807.d052sup4305mCG_5hmCGvHg38.bam",
  "assemblyNames": ["hg38"]
}
jbrowse add-track https://ont-open-data.s3.amazonaws.com/colo829_2024.03/basecalls/colo829bl/sup/PAU59807.d052sup4305mCG_5hmCGvHg38.bam \
  --trackId COLO829BL_normal_ont \
  --name "COLO829BL matched normal (ONT R10)" \
  --assemblyNames hg38

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

  • Main file: https://ont-open-data.s3.amazonaws.com/colo829_2024.03/basecalls/colo829bl/sup/PAU59807.d052sup4305mCG_5hmCGvHg38.bam

Click Next. JBrowse reads the adapter and track type off the file name. Then fill in:

  • Track name: COLO829BL matched normal (ONT R10)
  • Assembly: hg38

Click Add.

Open this track in JBrowse Web ↗

Open this track in JBrowse Desktop ↗ (JBrowse Desktop 5.0+)

The breakends come from the run's somatic SV calls, which need their .tbi beside them:

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

{
  "trackId": "COLO829_somatic_sv",
  "name": "COLO829 somatic SVs (nanomonsv)",
  "uri": "https://ont-open-data.s3.amazonaws.com/colo829_2024.03/wf_somatic_variation/sup/COLO829.wf-somatic-sv.vcf.gz",
  "assemblyNames": ["hg38"]
}
jbrowse add-track https://ont-open-data.s3.amazonaws.com/colo829_2024.03/wf_somatic_variation/sup/COLO829.wf-somatic-sv.vcf.gz \
  --trackId COLO829_somatic_sv \
  --name "COLO829 somatic SVs (nanomonsv)" \
  --assemblyNames hg38

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

  • Main file: https://ont-open-data.s3.amazonaws.com/colo829_2024.03/wf_somatic_variation/sup/COLO829.wf-somatic-sv.vcf.gz

Click Next. JBrowse reads the adapter and track type off the file name. Then fill in:

  • Track name: COLO829 somatic SVs (nanomonsv)
  • Assembly: hg38

Click Add.

Open this track in JBrowse Web ↗

Open this track in JBrowse Desktop ↗ (JBrowse Desktop 5.0+)

Open the SV calls and the tumor and normal read tracks at chr3:25,357,600-25,361,000. The tumor reads end in soft clipping, an end the aligner left unaligned, because every read crossing the junction continues on another chromosome. The matched normal is clean.

  • Show... → Show soft clipping in the track menu draws the clipped ends, which are off by default.
  • Sort by... → Split reads first lifts the reads that continue on another chromosome to the top of the pileup.
  • Force load approves the download when the track asks first because the pileup is deep, and holds 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.

Hand this to a coding agent. It rebuilds the figure above headlessly, and the session file is then the thing to edit: change the location or a track's settings, or add your own track under sessionTracks, and rerun.

The figure stacks 2 frames: one command draws each, and ImageMagick stacks them.

Frame 1

cat > session-1.json <<'JSON'
{
  "views": [
    {
      "type": "LinearGenomeView",
      "assembly": "hg38",
      "loc": "chr3:25,357,600-25,361,000",
      "tracks": [
        {
          "trackId": "COLO829_somatic_sv",
          "height": 130
        },
        {
          "trackId": "COLO829_tumor_ont",
          "type": "LinearAlignmentsDisplay",
          "forceLoad": true,
          "showSoftClipping": true,
          "height": 470,
          "featureHeight": 2
        },
        {
          "trackId": "COLO829BL_normal_ont",
          "type": "LinearAlignmentsDisplay",
          "forceLoad": true,
          "showSoftClipping": true,
          "height": 215,
          "featureHeight": 2
        }
      ]
    }
  ]
}
JSON

cat > callouts-1.json <<'JSON'
[
  {
    "type": "text",
    "text": "Right-click a breakend → Open breakpoint split view",
    "fontSize": 17,
    "maxWidth": 260,
    "leader": true,
    "anchor": {
      "selector": "[data-testid=\"feature-name-r_12_1\"]"
    },
    "dx": -30,
    "dy": 95
  }
]
JSON

npx @jbrowse/capture --instance https://jbrowse.org/code/jb2/main/ \
  --config https://jbrowse.org/demos/cancer_sv/config.json \
  --width 1000 --height 1126 \
  --spec session-1.json --annotations callouts-1.json -o frame-1.png

Frame 2

cat > session-2.json <<'JSON'
{
  "views": [
    {
      "type": "BreakpointSplitView",
      "displayName": "RARB (chr3) - BICC1 (chr10) - TRHDE (chr12)",
      "views": [
        {
          "assembly": "hg38",
          "loc": "chr3:25,354,568-25,364,568",
          "tracks": [
            {
              "trackId": "ncbi_refseq_hg38",
              "geneGlyphMode": "longestCoding",
              "height": 70
            },
            {
              "trackId": "COLO829_tumor_ont",
              "type": "LinearAlignmentsDisplay",
              "forceLoad": true,
              "showSoftClipping": true,
              "height": 160,
              "featureHeight": 1
            }
          ]
        },
        {
          "assembly": "hg38",
          "loc": "chr10:58,712,464-58,722,464",
          "tracks": [
            {
              "trackId": "ncbi_refseq_hg38",
              "geneGlyphMode": "longestCoding",
              "height": 70
            },
            {
              "trackId": "COLO829_tumor_ont",
              "type": "LinearAlignmentsDisplay",
              "forceLoad": true,
              "showSoftClipping": true,
              "height": 160,
              "featureHeight": 1
            }
          ]
        },
        {
          "assembly": "hg38",
          "loc": "chr12:72,268,294-72,278,294",
          "tracks": [
            {
              "trackId": "ncbi_refseq_hg38",
              "geneGlyphMode": "longestCoding",
              "height": 70
            },
            {
              "trackId": "COLO829_tumor_ont",
              "type": "LinearAlignmentsDisplay",
              "forceLoad": true,
              "showSoftClipping": true,
              "height": 160,
              "featureHeight": 1
            }
          ]
        }
      ]
    }
  ]
}
JSON

npx @jbrowse/capture --instance https://jbrowse.org/code/jb2/main/ \
  --config https://jbrowse.org/demos/cancer_sv/config.json \
  --width 1000 --height 1188 \
  --timeout 300000 \
  --spec session-2.json -o frame-2.png
magick frame-1.png frame-2.png -bordercolor white -border 12 +append figure.png

The figure's callouts across its frames are drawn over the stacked image, which these commands leave out.

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.

Following the chain across breakpoint split view panels

A breakpoint split view stacks the loci a rearrangement visits, one panel per locus, and draws the reads that leave one panel and arrive in another. Two ways to open one:

  • Add → Breakpoint split view builds it from loci you already know, one row per panel.
  • Right-click a record in the variant track and choose Open breakpoint split view. The dialog asks for the layout (two stacked panels, or one row spanning both breakends) and the window each panel opens at.

A breakend (BND) record names one partner, so on its own it opens two panels. Check Follow further breakends at each end to add the rest of the chain:

  • The dialog searches the callset at each end for another junction leaving from the same place and adds it when exactly one exists.
  • The search stops at a locus with two candidates, or at one leading back into the chain.
  • The search assumes two junctions leaving one locus belong to one molecule, and reads crossing both are the evidence.
  • From the chr3 record this chain starts at, the search finds three panels: the chr10 breakend has a second junction a couple of hundred bases away, and its far end is on chr12.
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 in JBrowse Web ↗Open in JBrowse Desktop ↗
Desktop link does nothing?

It needs JBrowse Desktop 5.0+. Or 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 loads a large dataset and takes a while to open.

Or rebuild it from your own data:

The short route: open the view in JBrowse Web, where File → Open track... adds your own files beside its hosted genome and tracks.

From scratch with your own data, the steps behind the figure:

  1. Open your genome: on the JBrowse Desktop start screen click Open new genome (or Show all available genomes to pick a hosted one). For JBrowse Web, jbrowse add-assembly puts it in your config.json.This figure uses hg38, loaded from a bgzip-compressed FASTA (.fa.gz + .fai + .gzi).
  2. Add a track: check one your config has in the track selector, or File → Open track... to paste a URL or choose a local file. This one needs a bgzip-compressed, tabix-indexed VCF (.vcf.gz + .tbi).This figure uses “COLO829 somatic SVs (nanomonsv)”.
  3. Add the next track the same way. This one needs a CRAM file (.cram + .crai).This figure uses “COLO829 tumour (ONT R10, haplotagged)”.
    1. Track menu → Read height → Super-compact
    2. 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.
  4. Type your region of interest into the location box and press Enter.This figure is at chr3:25,359,318-25,359,818.

This session spec draws the figure. It goes after &session=spec- on a JBrowse Web link that loads https://jbrowse.org/demos/cancer_sv/config.json, which is what the Web button above opens.

{
  "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
        }
      ]
    }
  ]
}

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

jbrowse-img draws the same view as an SVG, from the command line and without a browser. Point --config at your own config, or swap a track for your own file with --bam, --vcfgz and the other file flags.

npx @jbrowse/img --config https://jbrowse.org/demos/cancer_sv/config.json \
  --assembly hg38 --loc chr3:25,359,318-25,359,818 \
  --track COLO829_somatic_sv '{"height":130}' \
  --track COLO829_tumor_ont display:LinearAlignmentsDisplay '{"height":300,"featureHeight":1,"forceLoad":true}' \
  --width 900 --out figure.svg

--out figure.png writes a PNG instead, through rsvg-convert (apt install librsvg2-bin, brew install librsvg).

Hand this to a coding agent. It rebuilds the figure above headlessly, and the session file is then the thing to edit: change the location or a track's settings, or add your own track under sessionTracks, 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 \
  --width 900 --height 771 \
  --timeout 300000 \
  --spec session.json -o figure.png

The figure stacks 3 frames of a click-through; this command draws the view it starts from.

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.

To follow a single read, right-click it and choose Linear read vs ref. JBrowse opens a synteny view with the read as an assembly along the bottom and every locus it touches along the top, the layout Ribbon (Nattestad et al. 2021) introduced.

Assembling the der(3) derivative allele and aligning it to GRCh38

The cancer SV demo config, https://jbrowse.org/demos/cancer_sv/config.json, includes a der(3) contig assembled from the tumor reads that span all three loci, so every base in it comes from those reads.

To build one from your own data, pull the reads crossing the loci with samtools view, assemble them with Flye, Shasta or hifiasm, and align the contigs to the reference:

# asm5: same-species preset; -c: base-level CIGAR, to draw junctions at base scale
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 chr10 and chr12 pieces are templated insertions: stretches of other chromosomes copied in where the break was repaired.

Index the contigs, then load the contig as an assembly and the PAF as a synteny track between it and GRCh38:

samtools faidx contigs.fa

Goes in the assemblies array of config.json. See Assemblies.

{
  "name": "der3_RARB_BICC1_TRHDE",
  "uri": "contigs.fa"
}
jbrowse add-assembly contigs.fa \
  --name der3_RARB_BICC1_TRHDE \
  --load copy

In JBrowse Desktop, Open new genome on the start screen (or File → Open genome... in a session), then Open from a URL and paste, one per line:

contigs.fa
contigs.fa.fai

JBrowse reads the format off the file name. Then fill in:

  • Genome name: der3_RARB_BICC1_TRHDE

contigs.fa is relative to a config.json. Replace it with its URL or its path on this computer.

The track lists the query assembly (the contig) first and the target (GRCh38) second, the reverse of the minimap2 argument order. Reversed, the view opens empty and reports no error:

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

{
  "type": "SyntenyTrack",
  "trackId": "der3_vs_hg38",
  "name": "der3 contig vs hg38",
  "assemblyNames": ["der3_RARB_BICC1_TRHDE", "hg38"],
  "adapter": {
    "type": "PairwiseIndexedPAFAdapter",
    "uri": "der3.vs_reference.pif.gz",
    "queryAssembly": "der3_RARB_BICC1_TRHDE",
    "targetAssembly": "hg38"
  }
}
jbrowse add-track-json '{
  "type": "SyntenyTrack",
  "trackId": "der3_vs_hg38",
  "name": "der3 contig vs hg38",
  "assemblyNames": ["der3_RARB_BICC1_TRHDE", "hg38"],
  "adapter": {
    "type": "PairwiseIndexedPAFAdapter",
    "uri": "der3.vs_reference.pif.gz",
    "queryAssembly": "der3_RARB_BICC1_TRHDE",
    "targetAssembly": "hg38"
  }
}'

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

{
  "type": "SyntenyTrack",
  "trackId": "der3_vs_hg38",
  "name": "der3 contig vs hg38",
  "assemblyNames": ["der3_RARB_BICC1_TRHDE", "hg38"],
  "adapter": {
    "type": "PairwiseIndexedPAFAdapter",
    "uri": "der3.vs_reference.pif.gz",
    "queryAssembly": "der3_RARB_BICC1_TRHDE",
    "targetAssembly": "hg38"
  }
}

der3.vs_reference.pif.gz is relative to a config.json. Replace it with its URL or its path on this computer.

That shows it in the linear view. For the synteny view, open Add → Linear synteny view, pick the track under Quick start, and click Launch.

Add the truth set, called on five platforms before this ONT run existed, so every junction has an independent call to check against:

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

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

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

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

Open this track in JBrowse Web ↗

Open this track in JBrowse Desktop ↗ (JBrowse Desktop 5.0+)

The assembly, synteny track and truth set above reproduce the ribbons and arcs on your own contig; the segment labels, projected gene annotation and realigned reads below come from the demo's config.

Open Add → Linear synteny view with hg38 on the top row and der3_RARB_BICC1_TRHDE below, and pick der3 contig vs hg38 as the synteny track. The view shows:

  • ribbons colored by the reference chromosome each segment came from
  • a BED track on the derivative labelling each segment with its reference interval, which the gene track cannot do because a segment usually sits inside one large intron
  • the reference gene annotation projected onto the derivative: the first coding exon of RARB, a short stretch of TRHDE coding sequence in reverse, then RARB again, inverted
  • the tumor's split reads under the reference row, one row per molecule, with the truth set's validated calls above them
  • each junction drawn once as an arc, with a tick at each end over the sequence retained there. Ticks pointing apart mark a deletion-type join, ticks pointing toward each other a duplication-type join, and parallel ticks 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 in JBrowse Web ↗Open in JBrowse Desktop ↗
Desktop link does nothing?

It needs JBrowse Desktop 5.0+. Or 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%22uri%22%3A%22https%3A%2F%2Fzenodo.org%2Fapi%2Frecords%2F4716169%2Ffiles%2Ftruthset_somaticSVs_COLO829_hg38lifted.vcf%2Fcontent%22%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%22unit%22%3A%22chain%22%2C%22showBezierConnections%22%3Atrue%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%22color%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

Or rebuild it from your own data:

The short route: open the view in JBrowse Web, where File → Open track... adds your own files beside its hosted genome and tracks.

From scratch with your own data, the steps behind the figure:

  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. For JBrowse Web, run jbrowse add-assembly once for each to put them in your config.json.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. This one needs a bgzip-indexed PAF (.pif.gz + .tbi).A synteny track the session already has is quicker: pick it under Quick start, which fills in the rows itself.This figure uses “Derivative allele vs hg38”.
  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. Row 1 (hg38)
    1. Add a track: open this view's track selector and check one your config has, or click + and choose Add track to paste a URL or choose a local file. This one needs a bgzip-compressed, tabix-indexed GFF3 (.gff.gz + .tbi).This figure uses “NCBI RefSeq genes”.
      1. Track menu → Gene glyph → Representative transcript
      2. Track menu → Feature height → Compact
    2. Add the next track the same way. This one needs a VCF file (.vcf).This figure uses “COLO829 validated somatic SVs (Valle-Inclán 2022)”.
      1. Track menu → Feature height → Collapsed
    3. Add the next track the same way. This one needs a CRAM file (.cram + .crai).This figure uses “COLO829 tumour (ONT R10, haplotagged)”.
      1. 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.
      2. 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.
      3. Track menu → Read connections → View as pairs / link supplementary alignments (checked)
      4. 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.
      5. Track menu → Read height → Track sizing → Fixed read height + autogrow track height
      6. Drag the bottom edge of the coverage band to resize it.
      7. Track menu → Read height → Compact
      8. Track menu → Read connections → Read arcs
      9. 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.
      10. Track menu → Show... → Show legend (checked)
    4. Type your region of interest into the location box and press Enter.This figure is at chr3:25350000-25363000 chr10:58716500-58718500 chr12:72272000-72274500.
    5. View menu → Show... → Overlapping
    6. 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.
  10. Row 2 (der3_RARB_BICC1_TRHDE)
    1. Add a track: open this view's track selector and check one your config has, or click + and choose Add track to paste a URL or choose a local file. This one needs a bgzip-compressed, tabix-indexed BED (.bed.gz + .tbi).This figure uses “Where each segment came from”.
      1. Track menu → Feature height → Compact
    2. Add the next track the same way. This one needs features defined inline in the config.This figure uses “Reference genes projected onto the derivative”.
      1. Track menu → Gene glyph → Representative transcript
      2. Track menu → Feature height → Compact
    3. Type your region of interest into the location box and press Enter.This figure is at der3_RARB_BICC1_TRHDE:22,000-39,549.
    4. View menu → Show... → Offset

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",
    "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 Spec tab, or jbrowse set-default-session.

This session spec draws the figure. It goes after &session=spec- on a JBrowse Web link that loads https://jbrowse.org/demos/cancer_sv/config.json, which is what the Web button above opens.

{
  "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",
        "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"
              },
              "unit": "chain",
              "showBezierConnections": true,
              "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,
      "color": {
        "field": "reference"
      },
      "levelHeights": [
        88
      ]
    }
  ]
}

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",
                "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"
                            },
                            "unit": "chain",
                            "showBezierConnections": True,
                            "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,
            "color": {
                "field": "reference"
            },
            "levelHeights": [
                88
            ]
        }
    ],
)
app  # display the widget

jbrowse-img draws the same view as an SVG, from the command line and without a browser. Point --config at your own config, or swap a track for your own file with --bam, --vcfgz and the other file flags.

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

cat > session.json <<'JSON'
{
  "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"
              },
              "unit": "chain",
              "showBezierConnections": true,
              "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,
      "color": {
        "field": "reference"
      },
      "levelHeights": [
        88
      ]
    }
  ]
}
JSON

npx @jbrowse/img synteny --config https://jbrowse.org/demos/cancer_sv/config.json \
  --tracks tracks.json \
  --spec session.json \
  --width 1600 --out figure.svg

--out figure.png writes a PNG instead, through rsvg-convert (apt install librsvg2-bin, brew install librsvg).

Hand this to a coding agent. It rebuilds the figure above headlessly, and the session file is then the thing to edit: change the location or a track's settings, or add your own track under sessionTracks, 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",
        "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"
              },
              "unit": "chain",
              "showBezierConnections": true,
              "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,
      "color": {
        "field": "reference"
      },
      "levelHeights": [
        88
      ]
    }
  ]
}
JSON

cat > callouts.json <<'JSON'
[
  {
    "type": "text",
    "anchor": {
      "view": [
        0,
        1
      ],
      "trackId": "der3_genes",
      "fracY": 0,
      "alignX": "left",
      "dx": 40,
      "dy": 20
    },
    "text": "Fold-back: chr3, two short inserts, then the same chr3 stretch again, inverted",
    "fontSize": 18,
    "maxWidth": 900
  },
  {
    "type": "text",
    "text": "Dark rows: each molecule crosses this stretch twice, forward and then inverted",
    "fontSize": 17,
    "maxWidth": 380,
    "leader": true,
    "anchor": {
      "view": [
        0,
        0
      ],
      "trackId": "COLO829_tumor_ont",
      "loc": "chr3:25,356,000",
      "fracY": 0.8
    },
    "dx": -140,
    "dy": -30
  }
]
JSON

npx @jbrowse/capture --instance https://jbrowse.org/code/jb2/main/ \
  --config https://jbrowse.org/demos/cancer_sv/config.json \
  --width 1600 --height 895 \
  --spec session.json --annotations callouts.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 der(3) contig against the reads and the truth set

Zoom the synteny view to the kilobase holding the junctions, where the two inserts have separate ribbons. The truth set has a validated call at each place the split reads stop against hg38, and most of the same reads cross all three junctions in one alignment when realigned to the derivative.

The consensus was polished from these reads, so the realignment shows that they agree with each other. The truth set, called from other platforms, is the independent check.

Each hg38 window is wider than the piece the allele uses, and the read track shows split alignments only, so its coverage counts reads that cross a junction and steps down as each arm ends.

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 in JBrowse Web ↗Open in JBrowse Desktop ↗
Desktop link does nothing?

It needs JBrowse Desktop 5.0+. Or 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%22uri%22%3A%22https%3A%2F%2Fzenodo.org%2Fapi%2Frecords%2F4716169%2Ffiles%2Ftruthset_somaticSVs_COLO829_hg38lifted.vcf%2Fcontent%22%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%22unit%22%3A%22chain%22%2C%22showBezierConnections%22%3Atrue%2C%22heightMode%22%3A%22grow%22%2C%22height%22%3A170%2C%22featureHeight%22%3A5%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%22coverageHeight%22%3A40%2C%22unit%22%3A%22chain%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

Or rebuild it from your own data:

The short route: open the view in JBrowse Web, where File → Open track... adds your own files beside its hosted genome and tracks.

From scratch with your own data, the steps behind the figure:

  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. For JBrowse Web, run jbrowse add-assembly once for each to put them in your config.json.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. This one needs a bgzip-indexed PAF (.pif.gz + .tbi).A synteny track the session already has is quicker: pick it under Quick start, which fills in the rows itself.This figure uses “Derivative allele vs hg38”.
  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. Row 1 (hg38)
    1. Add a track: open this view's track selector and check one your config has, or click + and choose Add track to paste a URL or choose a local file. This one needs a bgzip-compressed, tabix-indexed GFF3 (.gff.gz + .tbi).This figure uses “NCBI RefSeq genes”.
      1. Track menu → Gene glyph → Representative transcript
      2. Track menu → Feature height → Compact
    2. Add the next track the same way. This one needs a VCF file (.vcf).This figure uses “COLO829 validated somatic SVs (Valle-Inclán 2022)”.
      1. Track menu → Feature height → Collapsed
    3. Add the next track the same way. This one needs a CRAM file (.cram + .crai).This figure uses “COLO829 tumour (ONT R10, haplotagged)”.
      1. 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.
      2. 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.
      3. Track menu → Read connections → View as pairs / link supplementary alignments (checked)
      4. 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.
      5. Track menu → Read height → Track sizing → Fixed read height + autogrow track height
      6. Track menu → Read height → Custom... → 5px
      7. Track menu → Show... → Show legend (checked)
      8. Track menu → Show... → Show coverage (checked)
      9. Drag the bottom edge of the coverage band to resize it.
      10. Track menu → Read connections → Read arcs
    4. Type your region of interest into the location box and press Enter.This figure is at chr3:25358500-25360100 chr10:58717200-58717920 chr12:72272880-72273520.
  9. Row 2 (der3_RARB_BICC1_TRHDE)
    1. Add a track: open this view's track selector and check one your config has, or click + and choose Add track to paste a URL or choose a local file. This one needs a bgzip-compressed, tabix-indexed BED (.bed.gz + .tbi).This figure uses “Where each segment came from”.
    2. Add the next track the same way. This one needs features defined inline in the config.This figure uses “Reference genes projected onto the derivative”.
      1. Track menu → Gene glyph → Representative transcript
      2. Track menu → Feature height → Compact
    3. Add the next track the same way. This one needs a BAM file (.bam + .bai).This figure uses “Spanning reads realigned to the derivative”.
      1. Track menu → Read height → Track sizing → Fixed read height + autogrow track height
      2. Track menu → Read height → Custom... → 5px
      3. Drag the bottom edge of the coverage band to resize it.
      4. Track menu → Read connections → View as pairs / link supplementary alignments (checked)
      5. Track menu → Filter by... → Edit filters...
    4. Type your region of interest into the location box and press Enter.This figure is at der3_RARB_BICC1_TRHDE:32,300-33,400.
    5. View menu → Show... → Show amino acids when zoomed in (unchecked)

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",
    "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 Spec tab, or jbrowse set-default-session.

This session spec draws the figure. It goes after &session=spec- on a JBrowse Web link that loads https://jbrowse.org/demos/cancer_sv/config.json, which is what the Web button above opens.

{
  "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",
        "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"
              },
              "unit": "chain",
              "showBezierConnections": true,
              "heightMode": "grow",
              "height": 170,
              "featureHeight": 5,
              "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,
              "coverageHeight": 40,
              "unit": "chain",
              "filterBy": {
                "flagInclude": 0,
                "flagExclude": 1796
              }
            }
          ]
        }
      ],
      "tracks": [
        [
          "der3_vs_hg38"
        ]
      ],
      "drawCurves": true,
      "levelHeights": [
        140
      ]
    }
  ]
}

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",
                "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"
                            },
                            "unit": "chain",
                            "showBezierConnections": True,
                            "heightMode": "grow",
                            "height": 170,
                            "featureHeight": 5,
                            "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,
                            "coverageHeight": 40,
                            "unit": "chain",
                            "filterBy": {
                                "flagInclude": 0,
                                "flagExclude": 1796
                            }
                        }
                    ]
                }
            ],
            "tracks": [
                [
                    "der3_vs_hg38"
                ]
            ],
            "drawCurves": True,
            "levelHeights": [
                140
            ]
        }
    ],
)
app  # display the widget

jbrowse-img draws the same view as an SVG, from the command line and without a browser. Point --config at your own config, or swap a track for your own file with --bam, --vcfgz and the other file flags.

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

cat > session.json <<'JSON'
{
  "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"
              },
              "unit": "chain",
              "showBezierConnections": true,
              "heightMode": "grow",
              "height": 170,
              "featureHeight": 5,
              "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,
              "coverageHeight": 40,
              "unit": "chain",
              "filterBy": {
                "flagInclude": 0,
                "flagExclude": 1796
              }
            }
          ]
        }
      ],
      "tracks": [
        [
          "der3_vs_hg38"
        ]
      ],
      "drawCurves": true,
      "levelHeights": [
        140
      ]
    }
  ]
}
JSON

npx @jbrowse/img synteny --config https://jbrowse.org/demos/cancer_sv/config.json \
  --tracks tracks.json \
  --spec session.json \
  --width 1600 --out figure.svg

--out figure.png writes a PNG instead, through rsvg-convert (apt install librsvg2-bin, brew install librsvg).

Hand this to a coding agent. It rebuilds the figure above headlessly, and the session file is then the thing to edit: change the location or a track's settings, or add your own track under sessionTracks, 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",
        "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"
              },
              "unit": "chain",
              "showBezierConnections": true,
              "heightMode": "grow",
              "height": 170,
              "featureHeight": 5,
              "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,
              "coverageHeight": 40,
              "unit": "chain",
              "filterBy": {
                "flagInclude": 0,
                "flagExclude": 1796
              }
            }
          ]
        }
      ],
      "tracks": [
        [
          "der3_vs_hg38"
        ]
      ],
      "drawCurves": true,
      "levelHeights": [
        140
      ]
    }
  ]
}
JSON

cat > callouts.json <<'JSON'
[
  {
    "type": "text",
    "text": "validated calls, where the reads stop",
    "fontSize": 17,
    "leader": true,
    "dx": 80,
    "anchor": {
      "view": [
        0,
        0
      ],
      "trackId": "COLO829_truth_set",
      "loc": "chr3:25,359,568",
      "fracY": 0.5
    }
  },
  {
    "type": "text",
    "text": "hg38, three source loci",
    "fontSize": 19,
    "anchor": {
      "view": [
        0,
        0
      ],
      "trackId": "ncbi_refseq_hg38",
      "loc": "chr3:25,358,800",
      "fracY": 0.75
    }
  },
  {
    "type": "text",
    "text": "the derivative allele",
    "fontSize": 19,
    "anchor": {
      "view": [
        0,
        1
      ],
      "trackId": "der3_genes",
      "alignX": "left",
      "dx": 10,
      "fracY": 0.95
    }
  }
]
JSON

npx @jbrowse/capture --instance https://jbrowse.org/code/jb2/main/ \
  --config https://jbrowse.org/demos/cancer_sv/config.json \
  --width 1600 --height 1355 \
  --spec session.json --annotations callouts.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.

COLO829 tumor ONT reads over one junction, twice. Against hg38 (left, split alignments only) they stop at the chr3 junction with their tails clipped; realigned to the derivative (right) they cross at flat depth. The panes are at different zooms.
Open in JBrowse Web ↗Open in JBrowse Desktop ↗
Desktop link does nothing?

It needs JBrowse Desktop 5.0+. Or 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 loads a large dataset and takes a while to open.

Or rebuild it from your own data:

The short route: open the view in JBrowse Web, where File → Open track... adds your own files beside its hosted genome and tracks.

From scratch with your own data, the steps behind the figure:

  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). For JBrowse Web, jbrowse add-assembly puts it in your config.json.This figure uses hg38, loaded from a bgzip-compressed FASTA (.fa.gz + .fai + .gzi).
  3. Add a track: open this view's track selector and check one your config has, or click + and choose Add track to paste a URL or choose a local file. This one needs a CRAM file (.cram + .crai).This figure uses “COLO829 tumour (ONT R10, haplotagged)”.
    1. 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.
    2. Track menu → Show... → Show soft clipping (checked)Reveals clipped bases — the signal that a read spans a breakpoint.
    3. 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.
    4. Track menu → Read height → Custom... → 2px
  4. Type your region of interest into the location box and press Enter.This figure is at chr3:25,357,000-25,362,000.
  5. Open your genome: on the JBrowse Desktop start screen click Open new genome (or Show all available genomes to pick a hosted one). For JBrowse Web, jbrowse add-assembly puts it in your config.json.This figure uses hg38, loaded from a bgzip-compressed FASTA (.fa.gz + .fai + .gzi).
  6. Add a track: open this view's track selector and check one your config has, or click + and choose Add track to paste a URL or choose a local file. This one needs a CRAM file (.cram + .crai).This figure uses “COLO829 tumour (ONT R10, haplotagged)”.
    1. 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.
    2. Track menu → Show... → Show soft clipping (checked)Reveals clipped bases — the signal that a read spans a breakpoint.
    3. 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.
    4. Track menu → Read height → Custom... → 2px
  7. Type your region of interest into the location box and press Enter.This figure is at chr10:58,715,000-58,720,000.
  8. Open your genome: on the JBrowse Desktop start screen click Open new genome (or Show all available genomes to pick a hosted one). For JBrowse Web, jbrowse add-assembly puts it in your config.json.This figure uses hg38, loaded from a bgzip-compressed FASTA (.fa.gz + .fai + .gzi).
  9. Add a track: open this view's track selector and check one your config has, or click + and choose Add track to paste a URL or choose a local file. This one needs a CRAM file (.cram + .crai).This figure uses “COLO829 tumour (ONT R10, haplotagged)”.
    1. 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.
    2. Track menu → Show... → Show soft clipping (checked)Reveals clipped bases — the signal that a read spans a breakpoint.
    3. 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.
    4. Track menu → Read height → Custom... → 2px
  10. 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 Spec tab.

This session spec draws the figure. It goes after &session=spec- on a JBrowse Web link that loads https://jbrowse.org/demos/cancer_sv/config.json, which is what the Web button above opens.

{
  "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
            }
          ]
        }
      ]
    }
  ]
}

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

jbrowse-img draws the same view as an SVG, from the command line and without a browser. Point --config at your own config, or swap a track for your own file with --bam, --vcfgz and the other file flags.

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/img breakpoint --config https://jbrowse.org/demos/cancer_sv/config.json \
  --spec session.json \
  --width 700 --out figure.svg

--out figure.png writes a PNG instead, through rsvg-convert (apt install librsvg2-bin, brew install librsvg).

Hand this to a coding agent. It rebuilds the figure above headlessly, and the session file is then the thing to edit: change the location or a track's settings, or add your own track under sessionTracks, and rerun.

The figure stacks 2 frames: one command draws each, and ImageMagick stacks them.

Frame 1: hg38

cat > session-1.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

cat > callouts-1.json <<'JSON'
[
  {
    "type": "circle",
    "text": "1",
    "anchor": {
      "view": [
        0,
        0
      ],
      "trackId": "COLO829_tumor_ont",
      "fracY": 0,
      "alignX": "left"
    },
    "radius": 15,
    "dx": 24,
    "dy": 78
  },
  {
    "type": "text",
    "text": "aligned to hg38",
    "anchor": {
      "view": [
        0,
        0
      ],
      "trackId": "COLO829_tumor_ont",
      "fracY": 0,
      "alignX": "left",
      "dx": 10,
      "dy": 30
    }
  }
]
JSON

npx @jbrowse/capture --instance https://jbrowse.org/code/jb2/main/ \
  --config https://jbrowse.org/demos/cancer_sv/config.json \
  --width 700 --height 833 \
  --timeout 300000 \
  --spec session-1.json --annotations callouts-1.json -o frame-1.png

Frame 2: derivative

cat > session-2.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

cat > callouts-2.json <<'JSON'
[
  {
    "type": "circle",
    "text": "2",
    "anchor": {
      "trackId": "reads_vs_der3",
      "fracY": 0,
      "alignX": "left"
    },
    "radius": 15,
    "dx": 24,
    "dy": 78
  },
  {
    "type": "text",
    "text": "realigned to the derived contig",
    "anchor": {
      "trackId": "reads_vs_der3",
      "fracY": 0,
      "alignX": "left",
      "dx": 10,
      "dy": 30
    }
  }
]
JSON

npx @jbrowse/capture --instance https://jbrowse.org/code/jb2/main/ \
  --config https://jbrowse.org/demos/cancer_sv/config.json \
  --width 700 --height 833 \
  --timeout 90000 \
  --spec session-2.json --annotations callouts-2.json -o frame-2.png
magick frame-1.png frame-2.png -bordercolor white -border 12 +append 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.

Open in JBrowse Web ↗Open in JBrowse Desktop ↗
Desktop link does nothing?

It needs JBrowse Desktop 5.0+. Or 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

Or rebuild it from your own data:

The short route: open the view in JBrowse Web, where File → Open track... adds your own files beside its hosted genome and tracks.

From scratch with your own data, the steps behind the figure:

  1. Open your genome: on the JBrowse Desktop start screen click Open new genome (or Show all available genomes to pick a hosted one). For JBrowse Web, jbrowse add-assembly puts it in your config.json.This figure uses der3_RARB_BICC1_TRHDE, loaded from a bgzip-compressed FASTA (.fa.gz + .fai + .gzi).
  2. Add a track: check one your config has in the track selector, or File → Open track... to paste a URL or choose a local file. This one needs a bgzip-compressed, tabix-indexed BED (.bed.gz + .tbi).This figure uses “Where each segment came from”.
  3. Add the next track the same way. This one needs a BAM file (.bam + .bai).This figure uses “Spanning reads realigned to the derivative”.
    1. Track menu → Show... → Show soft clipping (checked)Reveals clipped bases — the signal that a read spans a breakpoint.
    2. Track menu → Read height → Custom... → 8px
  4. Type your region of interest into the location box and press Enter.This figure is at der3_RARB_BICC1_TRHDE:32,545-32,925.
  5. 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.

This session spec draws the figure. It goes after &session=spec- on a JBrowse Web link that loads https://jbrowse.org/demos/cancer_sv/config.json, which is what the Web button above opens.

{
  "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
        }
      ]
    }
  ]
}

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

jbrowse-img draws the same view as an SVG, from the command line and without a browser. Point --config at your own config, or swap a track for your own file with --bam, --vcfgz and the other file flags.

npx @jbrowse/img --config https://jbrowse.org/demos/cancer_sv/config.json \
  --assembly der3_RARB_BICC1_TRHDE --loc der3_RARB_BICC1_TRHDE:32,545-32,925 \
  --track der3_segments '{"height":70}' \
  --track reads_vs_der3 display:LinearAlignmentsDisplay '{"showSoftClipping":true,"featureHeight":8,"height":470}' \
  --width 700 --out figure.svg

It has no flag for this figure's highlight, so its picture can differ there.

--out figure.png writes a PNG instead, through rsvg-convert (apt install librsvg2-bin, brew install librsvg).

Hand this to a coding agent. It rebuilds the figure above headlessly, and the session file is then the thing to edit: change the location or a track's settings, or add your own track under sessionTracks, and rerun.

The figure stacks 2 frames: one command draws each, and ImageMagick stacks them.

Frame 1: hg38

cat > session-1.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

cat > callouts-1.json <<'JSON'
[
  {
    "type": "circle",
    "text": "1",
    "anchor": {
      "view": [
        0,
        0
      ],
      "trackId": "COLO829_tumor_ont",
      "fracY": 0,
      "alignX": "left"
    },
    "radius": 15,
    "dx": 24,
    "dy": 78
  },
  {
    "type": "text",
    "text": "aligned to hg38",
    "anchor": {
      "view": [
        0,
        0
      ],
      "trackId": "COLO829_tumor_ont",
      "fracY": 0,
      "alignX": "left",
      "dx": 10,
      "dy": 30
    }
  }
]
JSON

npx @jbrowse/capture --instance https://jbrowse.org/code/jb2/main/ \
  --config https://jbrowse.org/demos/cancer_sv/config.json \
  --width 700 --height 833 \
  --timeout 300000 \
  --spec session-1.json --annotations callouts-1.json -o frame-1.png

Frame 2: derivative

cat > session-2.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

cat > callouts-2.json <<'JSON'
[
  {
    "type": "circle",
    "text": "2",
    "anchor": {
      "trackId": "reads_vs_der3",
      "fracY": 0,
      "alignX": "left"
    },
    "radius": 15,
    "dx": 24,
    "dy": 78
  },
  {
    "type": "text",
    "text": "realigned to the derived contig",
    "anchor": {
      "trackId": "reads_vs_der3",
      "fracY": 0,
      "alignX": "left",
      "dx": 10,
      "dy": 30
    }
  }
]
JSON

npx @jbrowse/capture --instance https://jbrowse.org/code/jb2/main/ \
  --config https://jbrowse.org/demos/cancer_sv/config.json \
  --width 700 --height 833 \
  --timeout 90000 \
  --spec session-2.json --annotations callouts-2.json -o frame-2.png
magick frame-1.png frame-2.png -bordercolor white -border 12 +append 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 into ./cancer_sv_build/jbrowse2. For COLO829 the script:

  1. Converts the coverage to bigWig as above.
  2. Adds the tumor and normal reads as tracks streamed from ONT's bucket.
  3. Downloads the published der(3) contig with its alignment to GRCh38, its segment labels and the spanning reads realigned to it.

The derivative allele shows how to assemble a contig like it from your own reads. The same run builds the K562 half of the demo, which Gene fusion calls and the DNA behind them walks through.

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

See also

Citations