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SV inspector view

TL;DR: The SV inspector is a combined variant table and whole-genome circular view for triaging structural variant calls. For an end-to-end walkthrough on real cancer sequencing data, see the C-GIAB tutorial.

Launch it from the Add menu in the main menu bar; an import form then asks for your SV data.

Launching the SV inspector from the Add menu. Open this view in JBrowse ↗

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

    Open this view in JBrowse Desktop ↗

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

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

    https://jbrowse.org/code/jb2/main/?config=https%3A%2F%2Fjbrowse.org%2Fdemos%2Fcgiab%2Fconfig.json&session=spec-%7B%22views%22%3A%5B%5D%7D&sessionName=JBrowse+docs%3A+sv_cgiab%2Ftranslocation_sv_inspector_start

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

    {
  "views": []
}

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

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

    cat > session.json <<'JSON'
{
  "views": []
}
JSON

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

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

    The following formats are supported:

    • VCF or VCF.gz (plain text or (b)gzipped)
    • BED, BEDPE
    • STAR-fusion result file

    The import form cannot infer STAR-Fusion from a .tsv extension, so that one needs its File Type set by hand; Gene fusion calls and the DNA behind them walks a caller's output through the inspector and out to the reads behind each call.

    Record types and compatible callers

    The SV inspector is best for long-range SV records: VCF entries with SVTYPE=BND (breakends; the VCF-spec way to encode translocations) or the caller-specific SVTYPE=TRA used by some tools.

    Single-locus deletions and duplications load into the table like anything else, but the circular overview cannot draw them: a chord runs between a record's two ends, and at whole-genome scale a deletion's two ends are the same point. The legend below the circle is what says so — it counts every class in the rows on screen, including the ones with no chord to draw, so a mostly-local callset reads as such.

    Compatible variant callers include:

    • Short-read - Manta, Delly, Lumpy
    • Long-read - pbsv, Sniffles

    Example workflow

    As an example, load this VCF of translocation events called from the SKBR3 breast cancer cell line (published data). Paste the URL into the import form and select hg19:

    The SV inspector import form with a VCF URL pasted. As the callout notes, 'Open from track' fills the inspector from a VCF track already open in the session. Open this view in JBrowse ↗

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

      Open this view in JBrowse Desktop ↗

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

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

      https://jbrowse.org/code/jb2/main/?config=test_data%2Fconfig_demo.json&session=spec-%7B%22views%22%3A%5B%7B%22type%22%3A%22SvInspectorView%22%7D%5D%7D&sessionName=JBrowse+docs%3A+sv_inspector_importform_after

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

      {
  "views": [
    {
      "type": "SvInspectorView"
    }
  ]
}

      Loaded against config: test_data/config_demo.json

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

      cat > session.json <<'JSON'
{
  "views": [
    {
      "type": "SvInspectorView"
    }
  ]
}
JSON

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

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

      SV inspector results

      The loaded file appears as a searchable table, one variant per row, alongside a whole-genome circular overview.

      The SV inspector with loaded results. Open this view in JBrowse ↗

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

      1. Open your genome: on the JBrowse Desktop start screen click Open new genome (or Show all available genomes to pick a hosted one).This figure uses hg19, loaded from a bgzip-compressed FASTA (.fa.gz + .fai + .gzi).
      2. Import form → Open file from URL or local computer → URL → Enter URL → OpenOpen the form with Add → SV inspector (or Add → Spreadsheet view); set File Type and Assembly in the same form before clicking Open.

      Open this view in JBrowse Desktop ↗

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

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

      https://jbrowse.org/code/jb2/main/?config=test_data%2Fconfig_demo.json&session=spec-%7B%22views%22%3A%5B%7B%22type%22%3A%22SvInspectorView%22%2C%22assembly%22%3A%22hg19%22%2C%22uri%22%3A%22https%3A%2F%2Fjbrowse.org%2Fgenomes%2Fhg19%2FSKBR3%2Freads_lr_skbr3.fa_ngmlr-0.2.3_mapped.bam.sniffles1kb_auto_l8_s5_noalt.filtered.vcf.gz%22%7D%5D%7D&sessionName=JBrowse+docs%3A+sv_inspector_importform_loaded

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

      {
  "views": [
    {
      "type": "SvInspectorView",
      "assembly": "hg19",
      "uri": "https://jbrowse.org/genomes/hg19/SKBR3/reads_lr_skbr3.fa_ngmlr-0.2.3_mapped.bam.sniffles1kb_auto_l8_s5_noalt.filtered.vcf.gz"
    }
  ]
}

      Loaded against config: test_data/config_demo.json

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

      cat > session.json <<'JSON'
{
  "views": [
    {
      "type": "SvInspectorView",
      "assembly": "hg19",
      "uri": "https://jbrowse.org/genomes/hg19/SKBR3/reads_lr_skbr3.fa_ngmlr-0.2.3_mapped.bam.sniffles1kb_auto_l8_s5_noalt.filtered.vcf.gz"
    }
  ]
}
JSON

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

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

      Table filters are reflected in the circular view.

      The SV inspector with filter applied. Open this view in JBrowse ↗

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

      1. Open your genome: on the JBrowse Desktop start screen click Open new genome (or Show all available genomes to pick a hosted one).This figure uses hg19, loaded from a bgzip-compressed FASTA (.fa.gz + .fai + .gzi).
      2. Import form → Open file from URL or local computer → URL → Enter URL → OpenOpen the form with Add → SV inspector (or Add → Spreadsheet view); set File Type and Assembly in the same form before clicking Open.

      Open this view in JBrowse Desktop ↗

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

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

      https://jbrowse.org/code/jb2/main/?config=test_data%2Fconfig_demo.json&session=spec-%7B%22views%22%3A%5B%7B%22type%22%3A%22SvInspectorView%22%2C%22assembly%22%3A%22hg19%22%2C%22uri%22%3A%22https%3A%2F%2Fjbrowse.org%2Fgenomes%2Fhg19%2FSKBR3%2Freads_lr_skbr3.fa_ngmlr-0.2.3_mapped.bam.sniffles1kb_auto_l8_s5_noalt.filtered.vcf.gz%22%7D%5D%7D&sessionName=JBrowse+docs%3A+sv_inspector_importform_filtered

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

      {
  "views": [
    {
      "type": "SvInspectorView",
      "assembly": "hg19",
      "uri": "https://jbrowse.org/genomes/hg19/SKBR3/reads_lr_skbr3.fa_ngmlr-0.2.3_mapped.bam.sniffles1kb_auto_l8_s5_noalt.filtered.vcf.gz"
    }
  ]
}

      Loaded against config: test_data/config_demo.json

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

      cat > session.json <<'JSON'
{
  "views": [
    {
      "type": "SvInspectorView",
      "assembly": "hg19",
      "uri": "https://jbrowse.org/genomes/hg19/SKBR3/reads_lr_skbr3.fa_ngmlr-0.2.3_mapped.bam.sniffles1kb_auto_l8_s5_noalt.filtered.vcf.gz"
    }
  ]
}
JSON

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

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

      The same callset from the Add menu onward: the import form, the URL and assembly it wants, the table and circle it opens, and a chromosome typed into the table filter taking the chords with it. Open the session this video starts in ↗

      Launching breakpoint split view

      Click a feature in the circular view, or the triangle dropdown on any table row, to open the breakpoint split view for that variant: two stacked linear genome views, each centered on one breakpoint. It opens empty; add alignment tracks to both via their track selectors, and the arcs and splines connecting supporting reads appear automatically.

      See also