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Variant track

TL;DR: A variant track displays VCF records, one glyph per call, and a click opens a per-sample genotype table. The track menu's Display types switches to a multi-sample view (one row per sample), an LD heatmap, or a paired-arc view for breakends. Color by... buckets variants by SnpEff/VEP consequence severity or SV type with one click, or colors by any INFO field via a jexl expression (e.g. minor allele frequency).

Variant track indicating an SNV alongside the alignment track evidence. 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 volvox, loaded from a .2bit genome.
  2. Add your own track: File → Open track..., then paste a URL or choose a local file. This one needs a bgzip-compressed, tabix-indexed VCF (.vcf.gz + .tbi).This figure uses “volvox filtered vcf”.
  3. Drag the bar at the bottom edge of the track to resize it.“volvox filtered vcf”.
  4. Add your own track: File → Open track..., then paste a URL or choose a local file. This one needs a CRAM file (.cram + .crai).This figure uses “volvox-sorted.cram (contigA, default display)”.
  5. Type your region of interest into the location box and press Enter.This figure is at ctgA:14439-14515.

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%2Fvolvox%2Fconfig.json&session=spec-%7B%22views%22%3A%5B%7B%22type%22%3A%22LinearGenomeView%22%2C%22assembly%22%3A%22volvox%22%2C%22loc%22%3A%22ctgA%3A14439-14515%22%2C%22tracks%22%3A%5B%7B%22trackId%22%3A%22volvox_filtered_vcf%22%2C%22height%22%3A60%7D%2C%22volvox_cram_alignments%22%5D%7D%5D%7D&sessionName=JBrowse+docs%3A+variant_with_pileup

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

{
  "views": [
    {
      "type": "LinearGenomeView",
      "assembly": "volvox",
      "loc": "ctgA:14439-14515",
      "tracks": [
        {
          "trackId": "volvox_filtered_vcf",
          "height": 60
        },
        "volvox_cram_alignments"
      ]
    }
  ]
}

Loaded against config: test_data/volvox/config.json

The same view with jbrowse-anywidget. Point the adapter at your own file.

from jbrowse_anywidget import LinearGenomeView, make_assembly

view = LinearGenomeView(
    assembly=make_assembly("volvox", "https://your-server/your-genome.fa.gz"),
    location="ctgA:14439-14515",
)

view.add_track({
    "type": "VariantTrack",
    "trackId": "my_track_1",
    "name": "My track 1",
    "assemblyNames": ["volvox"],
    "adapter": {"type": "VcfTabixAdapter", "uri": "https://your-server/your-file"},
})
view.add_track({
    "type": "AlignmentsTrack",
    "trackId": "my_track_2",
    "name": "My track 2",
    "assemblyNames": ["volvox"],
    "adapter": {"type": "CramAdapter", "uri": "https://your-server/your-file"},
})

view  # display the widget

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

cat > session.json <<'JSON'
{
  "views": [
    {
      "type": "LinearGenomeView",
      "assembly": "volvox",
      "loc": "ctgA:14439-14515",
      "tracks": [
        {
          "trackId": "volvox_filtered_vcf",
          "height": 60
        },
        "volvox_cram_alignments"
      ]
    }
  ]
}
JSON

npx @jbrowse/capture --instance https://jbrowse.org/code/jb2/main/ \
  --config https://jbrowse.org/code/jb2/main/test_data/volvox/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.

Display types

In a linear genome view, the track menu's Display types switches between:

  • Variant display, the default, covered on this page
  • Multi-sample variant display (regular) draws one row per sample at each variant's genomic position, the only multi-sample display that renders structural variants at scale
  • Multi-sample variant display (matrix) gives every visible variant a full column regardless of spacing, so shared haplotypes and runs of homozygosity show. Both are in the multi-sample variant guide
  • LD heatmap display computes pairwise r² from phased genotypes live. See the linkage disequilibrium tutorial
  • Paired arc display joins the two ends of each breakend record with an arc

In a circular view the same track gives a chord display, drawing breakends as chords across the ring.

Variant widget

Clicking a variant opens a widget with a per-sample genotype table.

Feature details panel for an SNV (C→T), with a per-sample genotype table in the SAMPLES section. 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 volvox, loaded from a .2bit genome.
  2. Add your own track: File → Open track..., then paste a URL or choose a local file. This one needs a bgzip-compressed, tabix-indexed VCF (.vcf.gz + .tbi).This figure uses “volvox 1000genomes vcf”.
  3. Type your region of interest into the location box and press Enter.This figure is at ctgA:6257-6305.

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%2Fvolvox%2Fconfig.json&session=spec-%7B%22views%22%3A%5B%7B%22type%22%3A%22LinearGenomeView%22%2C%22assembly%22%3A%22volvox%22%2C%22loc%22%3A%22ctgA%3A6257-6305%22%2C%22tracks%22%3A%5B%22volvox_test_vcf%22%5D%7D%5D%7D&sessionName=JBrowse+docs%3A+variant_panel

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

{
  "views": [
    {
      "type": "LinearGenomeView",
      "assembly": "volvox",
      "loc": "ctgA:6257-6305",
      "tracks": [
        "volvox_test_vcf"
      ]
    }
  ]
}

Loaded against config: test_data/volvox/config.json

The same view with jbrowse-anywidget. Point the adapter at your own file.

from jbrowse_anywidget import LinearGenomeView, make_assembly

view = LinearGenomeView(
    assembly=make_assembly("volvox", "https://your-server/your-genome.fa.gz"),
    location="ctgA:6257-6305",
)

view.add_track({
    "type": "VariantTrack",
    "trackId": "my_track",
    "name": "My track",
    "assemblyNames": ["volvox"],
    "adapter": {"type": "VcfTabixAdapter", "uri": "https://your-server/your-file"},
})

view  # display the widget

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

cat > session.json <<'JSON'
{
  "views": [
    {
      "type": "LinearGenomeView",
      "assembly": "volvox",
      "loc": "ctgA:6257-6305",
      "tracks": [
        "volvox_test_vcf"
      ]
    }
  ]
}
JSON

npx @jbrowse/capture --instance https://jbrowse.org/code/jb2/main/ \
  --config https://jbrowse.org/code/jb2/main/test_data/volvox/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 SAMPLES section lists every sample's genotype (GT) and other per-sample fields, with a plain-text or regex filter box per column. Typing '1' in the genotype filter keeps only samples carrying the first alternate allele (0|1 or 1|1). The 1000 Genomes SV tutorial filters a trio's genotypes this way to check whether a call is inherited.

Coloring variants

Color by... in the track menu:

  • Consequence impact buckets each variant by the severity of its most severe predicted consequence, read from SnpEff ANN or VEP CSQ in the INFO field: HIGH red, MODERATE orange, LOW yellow, MODIFIER grey
  • SV type colors by structural-variant class, with fixed colors per class and an ascending rainbow for copy-number alleles (<CN0>, <CN1>, ...)
  • Attribute... takes any attribute name and colors by its value, generating a jexl:randomColor(get(feature,'<attr>')) expression. Distinct values get distinct, stable colors, so it works on any categorical INFO field

The presets draw a dismissable color key naming the classes present, and work on the multi-sample displays too, where consequence impact and SV type list the terms in each tier and the color per class.

For anything else, set the display's color slot to a jexl expression. The variants plugin registers helpers for minor allele frequency, missingness and consequence impact; see helper functions for jexl color expressions.

See also