Skip to main content

Structural variants (Cancer GIAB) part 1: breakpoints

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.15. Desktop beta builds are coming soon.

The Cancer Genome in a Bottle project publishes HG008, a matched tumor/normal PDAC cell line, as PacBio HiFi reads, a draft SV and CNV benchmark, and a telomere-to-telomere assembly of the tumor. We read its structural variants against the reads and the assembly; part 2 reads its copy number. We:

  • load the benchmark SV calls and four further published SV callsets as variant tracks
  • align the tumor assembly to GRCh38 and load the alignment as a synteny track
  • open one chr3-chr13 translocation in the SV inspector and a breakpoint split view, and compare the tumor reads with the normal's
  • read a small heterozygous deletion in CUZD1 in a read pileup, beside ClinVar's copy-number variants
  • open the translocation in a dotplot and a linear synteny view of the assembly

Prerequisites

The walkthroughs at the end also run on the hosted C-GIAB demo. Building your own instance needs:

  • A JBrowse instance, from the web quickstart
  • A machine with HTTP access, either a public URL or http://localhost
  • ~1 TB of free disk for the tracks, or ~1.5 TB for the full pipeline
  • At least 32 GB of RAM for the minimap2 step; only data preparation needs it.
  • The command-line tools below, with the versions tested in parentheses: 
# Debian/Ubuntu
sudo apt install samtools minimap2 nodejs
# or conda, which has every tool above
conda install -c bioconda -c conda-forge samtools minimap2 nodejs
# any platform
npm install -g @jbrowse/cli

The data

HG008, the C-GIAB matched tumor/normal pair (NCBI BioProject PRJNA200694), is on the C-GIAB FTP, and the assemblies are on NIST's S3 bucket. The build script takes these files from their URLs, over 200 GB and hours of download. The page's commands build local files from them, and the tracks over those read them from disk; every other track reads a hosted copy. Each step takes your own tumor and normal reads in place of HG008's.

What it isFile
The C-GIAB reference build (GRCh38 with decoys and masked regions)GRCh38_GIABv3_no_alt_analysis_set_maskedGRC_decoys_MAP2K3_KMT2C_KCNJ18.fasta.gz
The tumor/normal PacBio HiFi reads (Revio run, 116x tumor, 35x normal)PacBio_Revio_20240125/
The V0.5 draft benchmark SV and CNV callsNIST_HG008-T_somatic-stvar-CNV_DraftBenchmark_V0.5-20260318/
Severus somatic SVs (HiFi)severus_somatic.vcf.gz
The minda ensemble SVs (HiFi, ONT and Illumina callers)HG008_minda_ensemble.vcf
DRAGEN's somatic SV calls (Illumina)standard/
NYGC's somatic SVs (Illumina)GRCh38-GIABv3/
The T2T tumor assembly, v3.2HG008T_v3.2.fasta.gz
The matched normal assembly, v6.3, which the build script leaves outHG008N_v6.3.fasta.gz

HG008, a pancreatic tumor and its matched normal

C-GIAB publishes HG008 from one pancreatic ductal adenocarcinoma (PDAC) donor, as the tumor (HG008-T) and normal pancreatic tissue (HG008-N-P). HG008-T is hypodiploid: 35 chromosomes down from 46, with widespread arm-level loss and truncal (present in every tumor cell) interchromosomal rearrangements (Wagner et al. 2026).

Assemblies: the C-GIAB GRCh38 reference and the tumor assembly

Every track below names one of two assemblies. The calls and reads sit on the C-GIAB GRCh38 build, GRCh38_GIABv3, which GIAB hosts BGZF-compressed with its .fai and .gzi, so the assembly reads it in place:

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

{
  "name": "GRCh38_GIABv3",
  "uri": "https://ftp-trace.ncbi.nlm.nih.gov/ReferenceSamples/giab/release/references/GRCh38/GRCh38_GIABv3_no_alt_analysis_set_maskedGRC_decoys_MAP2K3_KMT2C_KCNJ18.fasta.gz"
}
jbrowse add-assembly https://ftp-trace.ncbi.nlm.nih.gov/ReferenceSamples/giab/release/references/GRCh38/GRCh38_GIABv3_no_alt_analysis_set_maskedGRC_decoys_MAP2K3_KMT2C_KCNJ18.fasta.gz \
  --name GRCh38_GIABv3

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://ftp-trace.ncbi.nlm.nih.gov/ReferenceSamples/giab/release/references/GRCh38/GRCh38_GIABv3_no_alt_analysis_set_maskedGRC_decoys_MAP2K3_KMT2C_KCNJ18.fasta.gz
https://ftp-trace.ncbi.nlm.nih.gov/ReferenceSamples/giab/release/references/GRCh38/GRCh38_GIABv3_no_alt_analysis_set_maskedGRC_decoys_MAP2K3_KMT2C_KCNJ18.fasta.gz.fai
https://ftp-trace.ncbi.nlm.nih.gov/ReferenceSamples/giab/release/references/GRCh38/GRCh38_GIABv3_no_alt_analysis_set_maskedGRC_decoys_MAP2K3_KMT2C_KCNJ18.fasta.gz.gzi

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

  • Genome name: GRCh38_GIABv3

The synteny and dotplot sections use HG008T_v3.2, the T2T tumor assembly. NIST ships it BGZF-compressed, so samtools faidx writes the .fai and .gzi beside it without decompressing:

curl -LO https://nist-giab.s3.us-east-1.amazonaws.com/giab_tumor-normal/analysis/HG008/NIST_asm_dev/HG008T_v3.2/HG008T_v3.2.fasta.gz
samtools faidx HG008T_v3.2.fasta.gz

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

{
  "name": "HG008T_v3.2",
  "uri": "HG008T_v3.2.fasta.gz"
}
jbrowse add-assembly HG008T_v3.2.fasta.gz \
  --name HG008T_v3.2 \
  --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:

HG008T_v3.2.fasta.gz
HG008T_v3.2.fasta.gz.fai
HG008T_v3.2.fasta.gz.gzi

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

  • Genome name: HG008T_v3.2

HG008T_v3.2.fasta.gz is relative to a config.json. Replace it with its URL or its path on this computer.

The benchmark SV and CNV calls

The V0.5 HG008-T draft benchmark is an indexed VCF of SV calls and a BED of CNV calls, both loaded straight from their FTP URL.

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

{
  "trackId": "hg008t_benchmark_sv",
  "name": "HG008-T V0.5 draft benchmark somatic SVs",
  "uri": "https://ftp-trace.ncbi.nlm.nih.gov/ReferenceSamples/giab/data_somatic/HG008/Liss_lab/analysis/NIST_HG008-T_somatic-stvar-CNV_DraftBenchmark_V0.5-20260318/GRCh38_HG008-T-V0.5_somatic-stvar_PASS.draftbenchmark.vcf.gz",
  "assemblyNames": ["GRCh38_GIABv3"]
}
jbrowse add-track https://ftp-trace.ncbi.nlm.nih.gov/ReferenceSamples/giab/data_somatic/HG008/Liss_lab/analysis/NIST_HG008-T_somatic-stvar-CNV_DraftBenchmark_V0.5-20260318/GRCh38_HG008-T-V0.5_somatic-stvar_PASS.draftbenchmark.vcf.gz \
  --trackId hg008t_benchmark_sv \
  --name "HG008-T V0.5 draft benchmark somatic SVs" \
  --assemblyNames GRCh38_GIABv3

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://ftp-trace.ncbi.nlm.nih.gov/ReferenceSamples/giab/data_somatic/HG008/Liss_lab/analysis/NIST_HG008-T_somatic-stvar-CNV_DraftBenchmark_V0.5-20260318/GRCh38_HG008-T-V0.5_somatic-stvar_PASS.draftbenchmark.vcf.gz

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

  • Track name: HG008-T V0.5 draft benchmark somatic SVs
  • Assembly: GRCh38_GIABv3

Click Add.

The CNV BED has no header, so columnNames names its columns. In grammar-of-graphics terms, the track's color is a color scale that maps the field total_copy_number through the cuts in domain to the colors in range.

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

{
  "type": "FeatureTrack",
  "trackId": "hg008t_somatic_cnv",
  "name": "HG008-T somatic CNV",
  "assemblyNames": ["GRCh38_GIABv3"],
  "adapter": {
    "type": "BedAdapter",
    "uri": "https://ftp-trace.ncbi.nlm.nih.gov/ReferenceSamples/giab/data_somatic/HG008/Liss_lab/analysis/NIST_HG008-T_somatic-stvar-CNV_DraftBenchmark_V0.5-20260318/GRCh38_HG008-T-V0.5_somatic-CNV_PASS.draftbenchmark.calls.bed",
    "columnNames": [
      "chrom",
      "start",
      "end",
      "total_copy_number",
      "hap1_copy_number",
      "hap2_copy_number",
      "name"
    ]
  },
  "displayDefaults": {
    "labels": {
      "name": "jexl:'CN '+feature.total_copy_number+' ('+feature.hap1_copy_number+'|'+feature.hap2_copy_number+')'"
    },
    "color": {
      "field": "total_copy_number",
      "scale": "threshold",
      "domain": [1, 2, 3, 4],
      "range": ["#2166ac", "#92c5de", "#e0e0e0", "#f4a582", "#b2182b"],
      "labels": ["CN 0", "CN 1", "CN 2", "CN 3", "CN 4+"],
      "title": "Copy number"
    }
  }
}
jbrowse add-track-json '{
  "type": "FeatureTrack",
  "trackId": "hg008t_somatic_cnv",
  "name": "HG008-T somatic CNV",
  "assemblyNames": ["GRCh38_GIABv3"],
  "adapter": {
    "type": "BedAdapter",
    "uri": "https://ftp-trace.ncbi.nlm.nih.gov/ReferenceSamples/giab/data_somatic/HG008/Liss_lab/analysis/NIST_HG008-T_somatic-stvar-CNV_DraftBenchmark_V0.5-20260318/GRCh38_HG008-T-V0.5_somatic-CNV_PASS.draftbenchmark.calls.bed",
    "columnNames": [
      "chrom",
      "start",
      "end",
      "total_copy_number",
      "hap1_copy_number",
      "hap2_copy_number",
      "name"
    ]
  },
  "displayDefaults": {
    "labels": {
      "name": "jexl:'\''CN '\''+feature.total_copy_number+'\'' ('\''+feature.hap1_copy_number+'\''|'\''+feature.hap2_copy_number+'\'')'\''"
    },
    "color": {
      "field": "total_copy_number",
      "scale": "threshold",
      "domain": [1, 2, 3, 4],
      "range": ["#2166ac", "#92c5de", "#e0e0e0", "#f4a582", "#b2182b"],
      "labels": ["CN 0", "CN 1", "CN 2", "CN 3", "CN 4+"],
      "title": "Copy number"
    }
  }
}'

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": "FeatureTrack",
  "trackId": "hg008t_somatic_cnv",
  "name": "HG008-T somatic CNV",
  "assemblyNames": ["GRCh38_GIABv3"],
  "adapter": {
    "type": "BedAdapter",
    "uri": "https://ftp-trace.ncbi.nlm.nih.gov/ReferenceSamples/giab/data_somatic/HG008/Liss_lab/analysis/NIST_HG008-T_somatic-stvar-CNV_DraftBenchmark_V0.5-20260318/GRCh38_HG008-T-V0.5_somatic-CNV_PASS.draftbenchmark.calls.bed",
    "columnNames": [
      "chrom",
      "start",
      "end",
      "total_copy_number",
      "hap1_copy_number",
      "hap2_copy_number",
      "name"
    ]
  },
  "displayDefaults": {
    "labels": {
      "name": "jexl:'CN '+feature.total_copy_number+' ('+feature.hap1_copy_number+'|'+feature.hap2_copy_number+')'"
    },
    "color": {
      "field": "total_copy_number",
      "scale": "threshold",
      "domain": [1, 2, 3, 4],
      "range": ["#2166ac", "#92c5de", "#e0e0e0", "#f4a582", "#b2182b"],
      "labels": ["CN 0", "CN 1", "CN 2", "CN 3", "CN 4+"],
      "title": "Copy number"
    }
  }
}

Converting the HiFi reads to CRAM

The tumor and normal BAMs have no MD tags. Convert each to a local CRAM against the reference above:

# -T: the reference for the CRAM, the same build the assembly was loaded from
# --write-index: write the .crai in the same pass
samtools view HG008-T.bam --write-index -o HG008-T.cram -T GRCh38.fa

Each CRAM is a read track that decodes against GRCh38_GIABv3; the normal uses HG008-N.cram:

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

{
  "trackId": "HG008-T_hifi",
  "name": "HG008-T PacBio HiFi",
  "uri": "HG008-T.cram",
  "assemblyNames": ["GRCh38_GIABv3"]
}
jbrowse add-track HG008-T.cram \
  --trackId HG008-T_hifi \
  --name "HG008-T PacBio HiFi" \
  --assemblyNames GRCh38_GIABv3 \
  --load copy

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: HG008-T.cram

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

  • Track name: HG008-T PacBio HiFi
  • Assembly: GRCh38_GIABv3

Click Add.

HG008-T.cram is relative to a config.json. Replace it with its URL or its path on this computer.

Structural variants from the published callsets

C-GIAB publishes five somatic SV callsets for this pair, the benchmark among them:

CallsetCalled from
NIST V0.5 draft benchmarkassembly comparison plus read support
SeverusPacBio HiFi
minda ensembleeleven caller runs over HiFi, ONT and Illumina
DRAGENIllumina WGS
NYGC somatic pipeline (Manta and GRIDSS)Illumina WGS

Loading Severus and DRAGEN SV calls

Severus and DRAGEN are indexed VCFs with a record at each breakend, so they load with no display settings:

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

{
  "type": "VariantTrack",
  "trackId": "hg008t_severus_sv",
  "name": "HG008-T Severus somatic SVs (HiFi)",
  "assemblyNames": ["GRCh38_GIABv3"],
  "adapter": {
    "type": "VcfTabixAdapter",
    "uri": "https://ftp-trace.ncbi.nlm.nih.gov/ReferenceSamples/giab/data_somatic/HG008/Liss_lab/analysis/NIH_HiFi_Severus-SV_20240308/somatic_SVs/severus_somatic.vcf.gz"
  }
}
jbrowse add-track https://ftp-trace.ncbi.nlm.nih.gov/ReferenceSamples/giab/data_somatic/HG008/Liss_lab/analysis/NIH_HiFi_Severus-SV_20240308/somatic_SVs/severus_somatic.vcf.gz \
  --trackId hg008t_severus_sv \
  --name "HG008-T Severus somatic SVs (HiFi)" \
  --assemblyNames GRCh38_GIABv3

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://ftp-trace.ncbi.nlm.nih.gov/ReferenceSamples/giab/data_somatic/HG008/Liss_lab/analysis/NIH_HiFi_Severus-SV_20240308/somatic_SVs/severus_somatic.vcf.gz

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

  • Track name: HG008-T Severus somatic SVs (HiFi)
  • Assembly: GRCh38_GIABv3

Click Add.

Open this track in JBrowse Web ↗

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

{
  "type": "VariantTrack",
  "trackId": "hg008t_dragen_sv",
  "name": "HG008-T DRAGEN somatic SVs (Illumina)",
  "assemblyNames": ["GRCh38_GIABv3"],
  "adapter": {
    "type": "VcfTabixAdapter",
    "uri": "https://ftp-trace.ncbi.nlm.nih.gov/ReferenceSamples/giab/data_somatic/HG008/Liss_lab/analysis/DRAGEN-v4.2.4_ILMN-WGS_20240312/standard/dragen_4.2.4_HG008-mosaic_tumor.sv.vcf.gz"
  }
}
jbrowse add-track https://ftp-trace.ncbi.nlm.nih.gov/ReferenceSamples/giab/data_somatic/HG008/Liss_lab/analysis/DRAGEN-v4.2.4_ILMN-WGS_20240312/standard/dragen_4.2.4_HG008-mosaic_tumor.sv.vcf.gz \
  --trackId hg008t_dragen_sv \
  --name "HG008-T DRAGEN somatic SVs (Illumina)" \
  --assemblyNames GRCh38_GIABv3

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://ftp-trace.ncbi.nlm.nih.gov/ReferenceSamples/giab/data_somatic/HG008/Liss_lab/analysis/DRAGEN-v4.2.4_ILMN-WGS_20240312/standard/dragen_4.2.4_HG008-mosaic_tumor.sv.vcf.gz

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

  • Track name: HG008-T DRAGEN somatic SVs (Illumina)
  • Assembly: GRCh38_GIABv3

Click Add.

Open this track in JBrowse Web ↗

Loading the minda ensemble SV calls

The minda ensemble callset is a plain VCF, so VcfAdapter loads it whole, with no index:

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

{
  "type": "VariantTrack",
  "trackId": "hg008t_minda_sv",
  "name": "HG008-T minda ensemble SVs (HiFi, ONT, Illumina)",
  "assemblyNames": ["GRCh38_GIABv3"],
  "adapter": {
    "type": "VcfAdapter",
    "uri": "https://ftp-trace.ncbi.nlm.nih.gov/ReferenceSamples/giab/data_somatic/HG008/Liss_lab/analysis/NIH-NCI_minda-ensemble_20240710/HG008_minda_ensemble.vcf"
  }
}
jbrowse add-track https://ftp-trace.ncbi.nlm.nih.gov/ReferenceSamples/giab/data_somatic/HG008/Liss_lab/analysis/NIH-NCI_minda-ensemble_20240710/HG008_minda_ensemble.vcf \
  --trackId hg008t_minda_sv \
  --name "HG008-T minda ensemble SVs (HiFi, ONT, Illumina)" \
  --assemblyNames GRCh38_GIABv3

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://ftp-trace.ncbi.nlm.nih.gov/ReferenceSamples/giab/data_somatic/HG008/Liss_lab/analysis/NIH-NCI_minda-ensemble_20240710/HG008_minda_ensemble.vcf

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

  • Track name: HG008-T minda ensemble SVs (HiFi, ONT, Illumina)
  • Assembly: GRCh38_GIABv3

Click Add.

Open this track in JBrowse Web ↗

Drawing the NYGC SV calls (BEDPE) as arcs

BedpeAdapter reads a paired-end BED whole, with no index, and serves it to a variant track:

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

{
  "type": "VariantTrack",
  "trackId": "hg008t_nygc_sv",
  "name": "HG008-T NYGC somatic SVs (Manta, GRIDSS)",
  "assemblyNames": ["GRCh38_GIABv3"],
  "adapter": {
    "type": "BedpeAdapter",
    "uri": "https://ftp-trace.ncbi.nlm.nih.gov/ReferenceSamples/giab/data_somatic/HG008/Liss_lab/analysis/NYGC-somatic-pipeline_20240412/GRCh38-GIABv3/HG008-T--HG008-N.sv.annotated.v7.somatic.high_confidence.final.bedpe"
  },
  "displays": [
    {
      "type": "LinearMarkDisplay",
      "marks": [
        {
          "mark": "link",
          "encoding": { "size": 2 },
          "transform": [{ "type": "mate" }]
        }
      ]
    }
  ]
}
jbrowse add-track-json '{
  "type": "VariantTrack",
  "trackId": "hg008t_nygc_sv",
  "name": "HG008-T NYGC somatic SVs (Manta, GRIDSS)",
  "assemblyNames": ["GRCh38_GIABv3"],
  "adapter": {
    "type": "BedpeAdapter",
    "uri": "https://ftp-trace.ncbi.nlm.nih.gov/ReferenceSamples/giab/data_somatic/HG008/Liss_lab/analysis/NYGC-somatic-pipeline_20240412/GRCh38-GIABv3/HG008-T--HG008-N.sv.annotated.v7.somatic.high_confidence.final.bedpe"
  },
  "displays": [
    {
      "type": "LinearMarkDisplay",
      "marks": [
        {
          "mark": "link",
          "encoding": { "size": 2 },
          "transform": [{ "type": "mate" }]
        }
      ]
    }
  ]
}'

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": "hg008t_nygc_sv",
  "name": "HG008-T NYGC somatic SVs (Manta, GRIDSS)",
  "assemblyNames": ["GRCh38_GIABv3"],
  "adapter": {
    "type": "BedpeAdapter",
    "uri": "https://ftp-trace.ncbi.nlm.nih.gov/ReferenceSamples/giab/data_somatic/HG008/Liss_lab/analysis/NYGC-somatic-pipeline_20240412/GRCh38-GIABv3/HG008-T--HG008-N.sv.annotated.v7.somatic.high_confidence.final.bedpe"
  },
  "displays": [
    {
      "type": "LinearMarkDisplay",
      "marks": [
        {
          "mark": "link",
          "encoding": { "size": 2 },
          "transform": [{ "type": "mate" }]
        }
      ]
    }
  ]
}

Open chr3:139,970,000-140,005,000 with the five callsets loaded. A link whose other breakend lies outside the view draws as a short stem, as both NYGC records do below. The figure also shows the HiFiCNV depth, which part 2 builds.

One benchmark rearrangement's breakends in the SV callsets, over the HiFiCNV depth and the benchmark's CNV track.
Open in JBrowse Web ↗

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 GRCh38_GIABv3, 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 “HG008-T V0.5 draft benchmark somatic SVs”.
  3. Add the next track the same way. This one needs a bgzip-compressed, tabix-indexed VCF (.vcf.gz + .tbi).This figure uses “HG008-T Severus somatic SVs (HiFi)”.
    1. Track menu → Show... → Labels → None
  4. Add the next track the same way. This one needs a VCF file (.vcf).This figure uses “HG008-T minda ensemble SVs (HiFi, ONT, Illumina)”.
    1. Track menu → Show... → Labels → None
  5. Add the next track the same way. This one needs a bgzip-compressed, tabix-indexed VCF (.vcf.gz + .tbi).This figure uses “HG008-T DRAGEN somatic SVs (Illumina)”.
    1. Track menu → Show... → Labels → None
  6. Add the next track the same way. This one needs a BEDPE file (.bedpe).This figure uses “HG008-T NYGC somatic SVs (Manta, GRIDSS)”.
  7. Add the next track the same way. This one needs a BigWig file (.bw).This figure uses “HG008-T HiFiCNV depth”.
    1. Track menu → Plot type → XY plot
    2. Track menu → Edit colors/arrangement... → the plot color swatchesThe two colors the plot is drawn in, above and below the baseline; both the same paints a flat plot.
    3. Track menu → Resolution → Bin summary → Show min and max (unchecked)
    4. Track menu → Y axis... → RangePins the axis: Min 0 and Max 140. A field left empty follows the data in view.
    5. Track menu → Y axis... → Grid lines (checked)Absent in the density plot types, where score maps to color rather than height and a line would mark nothing.
  8. Add the next track the same way. This one needs a BED file (.bed).This figure uses “HG008-T somatic CNV”.
    1. Track menu → Advanced → Edit plot...
  9. Type your region of interest into the location box and press Enter.This figure is at chr3:139,970,000-140,005,000.
  10. 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": "QuantitativeTrack",
  "trackId": "hg008_depth",
  "name": "HG008-T HiFiCNV depth",
  "assemblyNames": [
    "GRCh38_GIABv3"
  ],
  "adapter": {
    "type": "BigWigAdapter",
    "bigWigLocation": {
      "uri": "https://jbrowse.org/demos/cgiab/HG008-T.hificnv.depth.bw",
      "locationType": "UriLocation"
    }
  }
}'

jbrowse add-track https://ftp-trace.ncbi.nlm.nih.gov/ReferenceSamples/giab/data_somatic/HG008/Liss_lab/analysis/NIH_HiFi_Severus-SV_20240308/somatic_SVs/severus_somatic.vcf.gz \
  --trackId hg008t_severus_sv \
  --name "HG008-T Severus somatic SVs (HiFi)" \
  --assemblyNames GRCh38_GIABv3

jbrowse add-track https://ftp-trace.ncbi.nlm.nih.gov/ReferenceSamples/giab/data_somatic/HG008/Liss_lab/analysis/NIH-NCI_minda-ensemble_20240710/HG008_minda_ensemble.vcf \
  --trackId hg008t_minda_sv \
  --name "HG008-T minda ensemble SVs (HiFi, ONT, Illumina)" \
  --assemblyNames GRCh38_GIABv3

jbrowse add-track https://ftp-trace.ncbi.nlm.nih.gov/ReferenceSamples/giab/data_somatic/HG008/Liss_lab/analysis/DRAGEN-v4.2.4_ILMN-WGS_20240312/standard/dragen_4.2.4_HG008-mosaic_tumor.sv.vcf.gz \
  --trackId hg008t_dragen_sv \
  --name "HG008-T DRAGEN somatic SVs (Illumina)" \
  --assemblyNames GRCh38_GIABv3

jbrowse add-track-json '{
  "type": "VariantTrack",
  "trackId": "hg008t_nygc_sv",
  "name": "HG008-T NYGC somatic SVs (Manta, GRIDSS)",
  "assemblyNames": [
    "GRCh38_GIABv3"
  ],
  "adapter": {
    "type": "BedpeAdapter",
    "uri": "https://ftp-trace.ncbi.nlm.nih.gov/ReferenceSamples/giab/data_somatic/HG008/Liss_lab/analysis/NYGC-somatic-pipeline_20240412/GRCh38-GIABv3/HG008-T--HG008-N.sv.annotated.v7.somatic.high_confidence.final.bedpe"
  },
  "displays": [
    {
      "type": "LinearMarkDisplay",
      "marks": [
        {
          "mark": "link",
          "encoding": {
            "size": 2
          },
          "transform": [
            {
              "type": "mate"
            }
          ]
        }
      ]
    }
  ]
}'

Run these where the config.json is, or add --out <dir>, and point each uri at your own file. The config needs GRCh38_GIABv3 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/cgiab/config.json, which is what the Web button above opens.

{
  "sessionTracks": [
    {
      "type": "QuantitativeTrack",
      "trackId": "hg008_depth",
      "name": "HG008-T HiFiCNV depth",
      "assemblyNames": [
        "GRCh38_GIABv3"
      ],
      "adapter": {
        "type": "BigWigAdapter",
        "bigWigLocation": {
          "uri": "https://jbrowse.org/demos/cgiab/HG008-T.hificnv.depth.bw",
          "locationType": "UriLocation"
        }
      }
    },
    {
      "type": "VariantTrack",
      "trackId": "hg008t_severus_sv",
      "name": "HG008-T Severus somatic SVs (HiFi)",
      "assemblyNames": [
        "GRCh38_GIABv3"
      ],
      "adapter": {
        "type": "VcfTabixAdapter",
        "uri": "https://ftp-trace.ncbi.nlm.nih.gov/ReferenceSamples/giab/data_somatic/HG008/Liss_lab/analysis/NIH_HiFi_Severus-SV_20240308/somatic_SVs/severus_somatic.vcf.gz"
      }
    },
    {
      "type": "VariantTrack",
      "trackId": "hg008t_minda_sv",
      "name": "HG008-T minda ensemble SVs (HiFi, ONT, Illumina)",
      "assemblyNames": [
        "GRCh38_GIABv3"
      ],
      "adapter": {
        "type": "VcfAdapter",
        "uri": "https://ftp-trace.ncbi.nlm.nih.gov/ReferenceSamples/giab/data_somatic/HG008/Liss_lab/analysis/NIH-NCI_minda-ensemble_20240710/HG008_minda_ensemble.vcf"
      }
    },
    {
      "type": "VariantTrack",
      "trackId": "hg008t_dragen_sv",
      "name": "HG008-T DRAGEN somatic SVs (Illumina)",
      "assemblyNames": [
        "GRCh38_GIABv3"
      ],
      "adapter": {
        "type": "VcfTabixAdapter",
        "uri": "https://ftp-trace.ncbi.nlm.nih.gov/ReferenceSamples/giab/data_somatic/HG008/Liss_lab/analysis/DRAGEN-v4.2.4_ILMN-WGS_20240312/standard/dragen_4.2.4_HG008-mosaic_tumor.sv.vcf.gz"
      }
    },
    {
      "type": "VariantTrack",
      "trackId": "hg008t_nygc_sv",
      "name": "HG008-T NYGC somatic SVs (Manta, GRIDSS)",
      "assemblyNames": [
        "GRCh38_GIABv3"
      ],
      "adapter": {
        "type": "BedpeAdapter",
        "uri": "https://ftp-trace.ncbi.nlm.nih.gov/ReferenceSamples/giab/data_somatic/HG008/Liss_lab/analysis/NYGC-somatic-pipeline_20240412/GRCh38-GIABv3/HG008-T--HG008-N.sv.annotated.v7.somatic.high_confidence.final.bedpe"
      },
      "displays": [
        {
          "type": "LinearMarkDisplay",
          "marks": [
            {
              "mark": "link",
              "encoding": {
                "size": 2
              },
              "transform": [
                {
                  "type": "mate"
                }
              ]
            }
          ]
        }
      ]
    }
  ],
  "views": [
    {
      "type": "LinearGenomeView",
      "assembly": "GRCh38_GIABv3",
      "loc": "chr3:139,970,000-140,005,000",
      "trackLabels": "offset",
      "tracks": [
        {
          "trackId": "hg008t_benchmark_sv",
          "type": "LinearVariantDisplay",
          "height": 55
        },
        {
          "trackId": "hg008t_severus_sv",
          "type": "LinearVariantDisplay",
          "showLabels": "none",
          "height": 45
        },
        {
          "trackId": "hg008t_minda_sv",
          "type": "LinearVariantDisplay",
          "showLabels": "none",
          "height": 45
        },
        {
          "trackId": "hg008t_dragen_sv",
          "type": "LinearVariantDisplay",
          "showLabels": "none",
          "height": 45
        },
        {
          "trackId": "hg008t_nygc_sv",
          "type": "LinearMarkDisplay",
          "height": 45
        },
        {
          "trackId": "hg008_depth",
          "type": "LinearWiggleDisplay",
          "mark": "bar",
          "color": "#0068d1",
          "extent": "none",
          "scales": {
            "y": {
              "domainMin": 0,
              "domainMax": 140,
              "grid": true
            }
          },
          "height": 180
        },
        {
          "trackId": "hg008t_somatic_cnv",
          "type": "LinearBasicDisplay",
          "color": {
            "field": "total_copy_number",
            "scale": "threshold",
            "domain": [
              1,
              2,
              3,
              4
            ],
            "range": [
              "#2166ac",
              "#92c5de",
              "#e0e0e0",
              "#f4a582",
              "#b2182b"
            ],
            "labels": [
              "CN 0",
              "CN 1",
              "CN 2",
              "CN 3",
              "CN 4+"
            ],
            "title": "Copy number"
          },
          "height": 120
        }
      ]
    }
  ]
}

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/cgiab/config.json")
app = JBrowseApp(
    assemblies=config["assemblies"],
    tracks=config.get("tracks", []) + [
        {
            "type": "QuantitativeTrack",
            "trackId": "hg008_depth",
            "name": "HG008-T HiFiCNV depth",
            "assemblyNames": [
                "GRCh38_GIABv3"
            ],
            "adapter": {
                "type": "BigWigAdapter",
                "bigWigLocation": {
                    "uri": "https://jbrowse.org/demos/cgiab/HG008-T.hificnv.depth.bw",
                    "locationType": "UriLocation"
                }
            }
        },
        {
            "type": "VariantTrack",
            "trackId": "hg008t_severus_sv",
            "name": "HG008-T Severus somatic SVs (HiFi)",
            "assemblyNames": [
                "GRCh38_GIABv3"
            ],
            "adapter": {
                "type": "VcfTabixAdapter",
                "uri": "https://ftp-trace.ncbi.nlm.nih.gov/ReferenceSamples/giab/data_somatic/HG008/Liss_lab/analysis/NIH_HiFi_Severus-SV_20240308/somatic_SVs/severus_somatic.vcf.gz"
            }
        },
        {
            "type": "VariantTrack",
            "trackId": "hg008t_minda_sv",
            "name": "HG008-T minda ensemble SVs (HiFi, ONT, Illumina)",
            "assemblyNames": [
                "GRCh38_GIABv3"
            ],
            "adapter": {
                "type": "VcfAdapter",
                "uri": "https://ftp-trace.ncbi.nlm.nih.gov/ReferenceSamples/giab/data_somatic/HG008/Liss_lab/analysis/NIH-NCI_minda-ensemble_20240710/HG008_minda_ensemble.vcf"
            }
        },
        {
            "type": "VariantTrack",
            "trackId": "hg008t_dragen_sv",
            "name": "HG008-T DRAGEN somatic SVs (Illumina)",
            "assemblyNames": [
                "GRCh38_GIABv3"
            ],
            "adapter": {
                "type": "VcfTabixAdapter",
                "uri": "https://ftp-trace.ncbi.nlm.nih.gov/ReferenceSamples/giab/data_somatic/HG008/Liss_lab/analysis/DRAGEN-v4.2.4_ILMN-WGS_20240312/standard/dragen_4.2.4_HG008-mosaic_tumor.sv.vcf.gz"
            }
        },
        {
            "type": "VariantTrack",
            "trackId": "hg008t_nygc_sv",
            "name": "HG008-T NYGC somatic SVs (Manta, GRIDSS)",
            "assemblyNames": [
                "GRCh38_GIABv3"
            ],
            "adapter": {
                "type": "BedpeAdapter",
                "uri": "https://ftp-trace.ncbi.nlm.nih.gov/ReferenceSamples/giab/data_somatic/HG008/Liss_lab/analysis/NYGC-somatic-pipeline_20240412/GRCh38-GIABv3/HG008-T--HG008-N.sv.annotated.v7.somatic.high_confidence.final.bedpe"
            },
            "displays": [
                {
                    "type": "LinearMarkDisplay",
                    "marks": [
                        {
                            "mark": "link",
                            "encoding": {
                                "size": 2
                            },
                            "transform": [
                                {
                                    "type": "mate"
                                }
                            ]
                        }
                    ]
                }
            ]
        }
    ],
    views=[
        {
            "type": "LinearGenomeView",
            "assembly": "GRCh38_GIABv3",
            "loc": "chr3:139,970,000-140,005,000",
            "trackLabels": "offset",
            "tracks": [
                {
                    "trackId": "hg008t_benchmark_sv",
                    "type": "LinearVariantDisplay",
                    "height": 55
                },
                {
                    "trackId": "hg008t_severus_sv",
                    "type": "LinearVariantDisplay",
                    "showLabels": "none",
                    "height": 45
                },
                {
                    "trackId": "hg008t_minda_sv",
                    "type": "LinearVariantDisplay",
                    "showLabels": "none",
                    "height": 45
                },
                {
                    "trackId": "hg008t_dragen_sv",
                    "type": "LinearVariantDisplay",
                    "showLabels": "none",
                    "height": 45
                },
                {
                    "trackId": "hg008t_nygc_sv",
                    "type": "LinearMarkDisplay",
                    "height": 45
                },
                {
                    "trackId": "hg008_depth",
                    "type": "LinearWiggleDisplay",
                    "mark": "bar",
                    "color": "#0068d1",
                    "extent": "none",
                    "scales": {
                        "y": {
                            "domainMin": 0,
                            "domainMax": 140,
                            "grid": True
                        }
                    },
                    "height": 180
                },
                {
                    "trackId": "hg008t_somatic_cnv",
                    "type": "LinearBasicDisplay",
                    "color": {
                        "field": "total_copy_number",
                        "scale": "threshold",
                        "domain": [
                            1,
                            2,
                            3,
                            4
                        ],
                        "range": [
                            "#2166ac",
                            "#92c5de",
                            "#e0e0e0",
                            "#f4a582",
                            "#b2182b"
                        ],
                        "labels": [
                            "CN 0",
                            "CN 1",
                            "CN 2",
                            "CN 3",
                            "CN 4+"
                        ],
                        "title": "Copy number"
                    },
                    "height": 120
                }
            ]
        }
    ],
)
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": "QuantitativeTrack",
    "trackId": "hg008_depth",
    "name": "HG008-T HiFiCNV depth",
    "assemblyNames": [
      "GRCh38_GIABv3"
    ],
    "adapter": {
      "type": "BigWigAdapter",
      "bigWigLocation": {
        "uri": "https://jbrowse.org/demos/cgiab/HG008-T.hificnv.depth.bw",
        "locationType": "UriLocation"
      }
    }
  },
  {
    "type": "VariantTrack",
    "trackId": "hg008t_severus_sv",
    "name": "HG008-T Severus somatic SVs (HiFi)",
    "assemblyNames": [
      "GRCh38_GIABv3"
    ],
    "adapter": {
      "type": "VcfTabixAdapter",
      "uri": "https://ftp-trace.ncbi.nlm.nih.gov/ReferenceSamples/giab/data_somatic/HG008/Liss_lab/analysis/NIH_HiFi_Severus-SV_20240308/somatic_SVs/severus_somatic.vcf.gz"
    }
  },
  {
    "type": "VariantTrack",
    "trackId": "hg008t_minda_sv",
    "name": "HG008-T minda ensemble SVs (HiFi, ONT, Illumina)",
    "assemblyNames": [
      "GRCh38_GIABv3"
    ],
    "adapter": {
      "type": "VcfAdapter",
      "uri": "https://ftp-trace.ncbi.nlm.nih.gov/ReferenceSamples/giab/data_somatic/HG008/Liss_lab/analysis/NIH-NCI_minda-ensemble_20240710/HG008_minda_ensemble.vcf"
    }
  },
  {
    "type": "VariantTrack",
    "trackId": "hg008t_dragen_sv",
    "name": "HG008-T DRAGEN somatic SVs (Illumina)",
    "assemblyNames": [
      "GRCh38_GIABv3"
    ],
    "adapter": {
      "type": "VcfTabixAdapter",
      "uri": "https://ftp-trace.ncbi.nlm.nih.gov/ReferenceSamples/giab/data_somatic/HG008/Liss_lab/analysis/DRAGEN-v4.2.4_ILMN-WGS_20240312/standard/dragen_4.2.4_HG008-mosaic_tumor.sv.vcf.gz"
    }
  },
  {
    "type": "VariantTrack",
    "trackId": "hg008t_nygc_sv",
    "name": "HG008-T NYGC somatic SVs (Manta, GRIDSS)",
    "assemblyNames": [
      "GRCh38_GIABv3"
    ],
    "adapter": {
      "type": "BedpeAdapter",
      "uri": "https://ftp-trace.ncbi.nlm.nih.gov/ReferenceSamples/giab/data_somatic/HG008/Liss_lab/analysis/NYGC-somatic-pipeline_20240412/GRCh38-GIABv3/HG008-T--HG008-N.sv.annotated.v7.somatic.high_confidence.final.bedpe"
    },
    "displays": [
      {
        "type": "LinearMarkDisplay",
        "marks": [
          {
            "mark": "link",
            "encoding": {
              "size": 2
            },
            "transform": [
              {
                "type": "mate"
              }
            ]
          }
        ]
      }
    ]
  }
]
JSON

npx @jbrowse/img --config https://jbrowse.org/demos/cgiab/config.json \
  --tracks tracks.json \
  --assembly GRCh38_GIABv3 --loc chr3:139,970,000-140,005,000 \
  --trackLabels offset \
  --track hg008t_benchmark_sv display:LinearVariantDisplay '{"height":55}' \
  --track hg008t_severus_sv display:LinearVariantDisplay '{"showLabels":"none","height":45}' \
  --track hg008t_minda_sv display:LinearVariantDisplay '{"showLabels":"none","height":45}' \
  --track hg008t_dragen_sv display:LinearVariantDisplay '{"showLabels":"none","height":45}' \
  --track hg008t_nygc_sv display:LinearMarkDisplay '{"height":45}' \
  --track hg008_depth display:LinearWiggleDisplay '{"mark":"bar","color":"#0068d1","extent":"none","scales":{"y":{"domainMin":0,"domainMax":140,"grid":true}},"height":180}' \
  --track hg008t_somatic_cnv display:LinearBasicDisplay '{"color":{"field":"total_copy_number","scale":"threshold","domain":[1,2,3,4],"range":["#2166ac","#92c5de","#e0e0e0","#f4a582","#b2182b"],"labels":["CN 0","CN 1","CN 2","CN 3","CN 4+"],"title":"Copy number"},"height":120}' \
  --width 1500 --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": "QuantitativeTrack",
      "trackId": "hg008_depth",
      "name": "HG008-T HiFiCNV depth",
      "assemblyNames": [
        "GRCh38_GIABv3"
      ],
      "adapter": {
        "type": "BigWigAdapter",
        "bigWigLocation": {
          "uri": "https://jbrowse.org/demos/cgiab/HG008-T.hificnv.depth.bw",
          "locationType": "UriLocation"
        }
      }
    },
    {
      "type": "VariantTrack",
      "trackId": "hg008t_severus_sv",
      "name": "HG008-T Severus somatic SVs (HiFi)",
      "assemblyNames": [
        "GRCh38_GIABv3"
      ],
      "adapter": {
        "type": "VcfTabixAdapter",
        "uri": "https://ftp-trace.ncbi.nlm.nih.gov/ReferenceSamples/giab/data_somatic/HG008/Liss_lab/analysis/NIH_HiFi_Severus-SV_20240308/somatic_SVs/severus_somatic.vcf.gz"
      }
    },
    {
      "type": "VariantTrack",
      "trackId": "hg008t_minda_sv",
      "name": "HG008-T minda ensemble SVs (HiFi, ONT, Illumina)",
      "assemblyNames": [
        "GRCh38_GIABv3"
      ],
      "adapter": {
        "type": "VcfAdapter",
        "uri": "https://ftp-trace.ncbi.nlm.nih.gov/ReferenceSamples/giab/data_somatic/HG008/Liss_lab/analysis/NIH-NCI_minda-ensemble_20240710/HG008_minda_ensemble.vcf"
      }
    },
    {
      "type": "VariantTrack",
      "trackId": "hg008t_dragen_sv",
      "name": "HG008-T DRAGEN somatic SVs (Illumina)",
      "assemblyNames": [
        "GRCh38_GIABv3"
      ],
      "adapter": {
        "type": "VcfTabixAdapter",
        "uri": "https://ftp-trace.ncbi.nlm.nih.gov/ReferenceSamples/giab/data_somatic/HG008/Liss_lab/analysis/DRAGEN-v4.2.4_ILMN-WGS_20240312/standard/dragen_4.2.4_HG008-mosaic_tumor.sv.vcf.gz"
      }
    },
    {
      "type": "VariantTrack",
      "trackId": "hg008t_nygc_sv",
      "name": "HG008-T NYGC somatic SVs (Manta, GRIDSS)",
      "assemblyNames": [
        "GRCh38_GIABv3"
      ],
      "adapter": {
        "type": "BedpeAdapter",
        "uri": "https://ftp-trace.ncbi.nlm.nih.gov/ReferenceSamples/giab/data_somatic/HG008/Liss_lab/analysis/NYGC-somatic-pipeline_20240412/GRCh38-GIABv3/HG008-T--HG008-N.sv.annotated.v7.somatic.high_confidence.final.bedpe"
      },
      "displays": [
        {
          "type": "LinearMarkDisplay",
          "marks": [
            {
              "mark": "link",
              "encoding": {
                "size": 2
              },
              "transform": [
                {
                  "type": "mate"
                }
              ]
            }
          ]
        }
      ]
    }
  ],
  "views": [
    {
      "type": "LinearGenomeView",
      "assembly": "GRCh38_GIABv3",
      "loc": "chr3:139,970,000-140,005,000",
      "trackLabels": "offset",
      "tracks": [
        {
          "trackId": "hg008t_benchmark_sv",
          "type": "LinearVariantDisplay",
          "height": 55
        },
        {
          "trackId": "hg008t_severus_sv",
          "type": "LinearVariantDisplay",
          "showLabels": "none",
          "height": 45
        },
        {
          "trackId": "hg008t_minda_sv",
          "type": "LinearVariantDisplay",
          "showLabels": "none",
          "height": 45
        },
        {
          "trackId": "hg008t_dragen_sv",
          "type": "LinearVariantDisplay",
          "showLabels": "none",
          "height": 45
        },
        {
          "trackId": "hg008t_nygc_sv",
          "type": "LinearMarkDisplay",
          "height": 45
        },
        {
          "trackId": "hg008_depth",
          "type": "LinearWiggleDisplay",
          "mark": "bar",
          "color": "#0068d1",
          "extent": "none",
          "scales": {
            "y": {
              "domainMin": 0,
              "domainMax": 140,
              "grid": true
            }
          },
          "height": 180
        },
        {
          "trackId": "hg008t_somatic_cnv",
          "type": "LinearBasicDisplay",
          "color": {
            "field": "total_copy_number",
            "scale": "threshold",
            "domain": [
              1,
              2,
              3,
              4
            ],
            "range": [
              "#2166ac",
              "#92c5de",
              "#e0e0e0",
              "#f4a582",
              "#b2182b"
            ],
            "labels": [
              "CN 0",
              "CN 1",
              "CN 2",
              "CN 3",
              "CN 4+"
            ],
            "title": "Copy number"
          },
          "height": 120
        }
      ]
    }
  ]
}
JSON

npx @jbrowse/capture --instance https://jbrowse.org/code/jb2/main/ \
  --config https://jbrowse.org/demos/cgiab/config.json \
  --width 1500 --height 984 \
  --timeout 180000 \
  --spec 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.

Aligning the tumor assembly to GRCh38

The tumor assembly is haplotype-resolved into T2T scaffolds. The synteny and dotplot views draw its alignment to GRCh38, a PAF file:

# asm5: minimap2's preset for an assembly against a reference of the same species
# -c: write base-level CIGARs
minimap2 -cx asm5 GRCh38.fa HG008T_v3.2.fasta > HG008T_v3.2.paf

The track lists the query assembly (the tumor assembly) 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": "HG008T_v3.2_paf",
  "name": "HG008T_v3.2 vs GRCh38_GIABv3",
  "assemblyNames": ["HG008T_v3.2", "GRCh38_GIABv3"],
  "adapter": {
    "type": "PAFAdapter",
    "uri": "HG008T_v3.2.paf"
  }
}
jbrowse add-track HG008T_v3.2.paf \
  --trackId HG008T_v3.2_paf \
  --name "HG008T_v3.2 vs GRCh38_GIABv3" \
  --assemblyNames HG008T_v3.2,GRCh38_GIABv3 \
  --load copy

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": "HG008T_v3.2_paf",
  "name": "HG008T_v3.2 vs GRCh38_GIABv3",
  "assemblyNames": ["HG008T_v3.2", "GRCh38_GIABv3"],
  "adapter": {
    "type": "PAFAdapter",
    "uri": "HG008T_v3.2.paf"
  }
}

HG008T_v3.2.paf 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.

The matched normal assembly (HG008N_v6.3.fasta.gz, same S3 path) loads the same way, as the synteny track config guide shows.

Checking SV calls against reads and the assembly

A chr3-chr13 translocation: breakpoint reads and the tumor contig

Add → SV inspector, then Open from track to pick the C-GIAB benchmark VCF loaded earlier.

The SV inspector showing the benchmark VCF as a circular overview alongside a table of calls.
Open in JBrowse Web ↗

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 GRCh38_GIABv3, 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.
  3. Drag the bar at the bottom edge of the view to resize it (1000px here).

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

{
  "views": [
    {
      "type": "SvInspectorView",
      "assembly": "GRCh38_GIABv3",
      "uri": "https://jbrowse.org/genomes/GRCh38/cgiab/GRCh38_HG008-T-V0.5_somatic-stvar_PASS.draftbenchmark.vcf.gz",
      "height": 1000
    }
  ]
}

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/cgiab/config.json")
app = JBrowseApp(
    assemblies=config["assemblies"],
    tracks=config.get("tracks", []),
    views=[
        {
            "type": "SvInspectorView",
            "assembly": "GRCh38_GIABv3",
            "uri": "https://jbrowse.org/genomes/GRCh38/cgiab/GRCh38_HG008-T-V0.5_somatic-stvar_PASS.draftbenchmark.vcf.gz",
            "height": 1000
        }
    ],
)
app  # display the widget

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

cat > session.json <<'JSON'
{
  "views": [
    {
      "type": "SvInspectorView",
      "assembly": "GRCh38_GIABv3",
      "uri": "https://jbrowse.org/genomes/GRCh38/cgiab/GRCh38_HG008-T-V0.5_somatic-stvar_PASS.draftbenchmark.vcf.gz",
      "height": 1000
    }
  ]
}
JSON

npx @jbrowse/capture --instance https://jbrowse.org/code/jb2/main/ \
  --config https://jbrowse.org/demos/cgiab/config.json \
  --width 1500 --height 1065 \
  --spec session.json -o figure.png

The figure's clicks scroll the table to SV_20, which this command does not do, so its picture differs there.

It leaves out 2 callouts anchored to what the clicks bring up.

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_20 and SV_190 are the two records of one breakpoint, where chr3:139,976,414 joins chr13:114,353,244. The benchmark files them under EVENT=cluster_3 with two further breakends and tags the cluster EVENTTYPE=CHROMOPLEXY (rearrangements chained across chromosomes). To read the junction in the reads:

  • Choose cluster_3 under Filter by event, then click the chord joining chr3 and chr13 to launch the breakpoint split view.
  • Set Read height → Compact on the tumor PacBio HiFi reads opened on each panel.
  • Sort by... → Split reads first lifts the split reads to the top of each pileup.

The cancer SV tutorial covers opening the view from a record and following the further breakends.

Breakpoint split view of the chr3-chr13 translocation with tumor HiFi reads. Splines join the two halves of each split read.
Open in JBrowse Web ↗

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 GRCh38_GIABv3, loaded from a bgzip-compressed FASTA (.fa.gz + .fai + .gzi).
  2. 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 VCF (.vcf.gz + .tbi).This figure uses “HG008-T V0.5 draft benchmark somatic SVs”.
  3. Add the next track the same way. This one needs a BAM file (.bam + .bai).This figure uses “HG008-T_PacBio-HiFi-Revio_20240125_116x_GRCh38-GIABv3”.
    1. Track menu → Read height → Super-compact
    2. Track menu → Read connections → Off-screen mate connections → Hide off-screen mate connectionsThe row stays greyed out until an arc or read-cloud overlay, or the curved connectors, are on.
    3. 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 chr3:139,971,414-139,981,414.
  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 GRCh38_GIABv3, 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 bgzip-compressed, tabix-indexed VCF (.vcf.gz + .tbi).This figure uses “HG008-T V0.5 draft benchmark somatic SVs”.
  7. Add the next track the same way. This one needs a BAM file (.bam + .bai).This figure uses “HG008-T_PacBio-HiFi-Revio_20240125_116x_GRCh38-GIABv3”.
    1. Track menu → Read height → Super-compact
    2. Track menu → Read connections → Off-screen mate connections → Hide off-screen mate connectionsThe row stays greyed out until an arc or read-cloud overlay, or the curved connectors, are on.
    3. 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.
  8. Type your region of interest into the location box and press Enter.This figure is at chr13:114,348,244-114,358,244.

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

{
  "views": [
    {
      "type": "BreakpointSplitView",
      "views": [
        {
          "loc": "chr3:139,971,414-139,981,414",
          "assembly": "GRCh38_GIABv3",
          "tracks": [
            {
              "trackId": "hg008t_benchmark_sv",
              "type": "LinearVariantDisplay",
              "height": 40
            },
            {
              "trackId": "HG008-T_PacBio-HiFi-Revio_20240125_116x_GRCh38-GIABv3",
              "type": "LinearAlignmentsDisplay",
              "pileup": {
                "readHeight": 1
              },
              "filter": {
                "connections": {
                  "offscreenMates": "exclude"
                }
              },
              "height": 200,
              "forceLoad": true
            }
          ]
        },
        {
          "loc": "chr13:114,348,244-114,358,244",
          "assembly": "GRCh38_GIABv3",
          "tracks": [
            {
              "trackId": "hg008t_benchmark_sv",
              "type": "LinearVariantDisplay",
              "height": 40
            },
            {
              "trackId": "HG008-T_PacBio-HiFi-Revio_20240125_116x_GRCh38-GIABv3",
              "type": "LinearAlignmentsDisplay",
              "pileup": {
                "readHeight": 1
              },
              "filter": {
                "connections": {
                  "offscreenMates": "exclude"
                }
              },
              "height": 200,
              "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/cgiab/config.json")
app = JBrowseApp(
    assemblies=config["assemblies"],
    tracks=config.get("tracks", []),
    views=[
        {
            "type": "BreakpointSplitView",
            "views": [
                {
                    "loc": "chr3:139,971,414-139,981,414",
                    "assembly": "GRCh38_GIABv3",
                    "tracks": [
                        {
                            "trackId": "hg008t_benchmark_sv",
                            "type": "LinearVariantDisplay",
                            "height": 40
                        },
                        {
                            "trackId": "HG008-T_PacBio-HiFi-Revio_20240125_116x_GRCh38-GIABv3",
                            "type": "LinearAlignmentsDisplay",
                            "pileup": {
                                "readHeight": 1
                            },
                            "filter": {
                                "connections": {
                                    "offscreenMates": "exclude"
                                }
                            },
                            "height": 200,
                            "forceLoad": True
                        }
                    ]
                },
                {
                    "loc": "chr13:114,348,244-114,358,244",
                    "assembly": "GRCh38_GIABv3",
                    "tracks": [
                        {
                            "trackId": "hg008t_benchmark_sv",
                            "type": "LinearVariantDisplay",
                            "height": 40
                        },
                        {
                            "trackId": "HG008-T_PacBio-HiFi-Revio_20240125_116x_GRCh38-GIABv3",
                            "type": "LinearAlignmentsDisplay",
                            "pileup": {
                                "readHeight": 1
                            },
                            "filter": {
                                "connections": {
                                    "offscreenMates": "exclude"
                                }
                            },
                            "height": 200,
                            "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.

cat > session.json <<'JSON'
{
  "views": [
    {
      "type": "BreakpointSplitView",
      "views": [
        {
          "loc": "chr3:139,971,414-139,981,414",
          "assembly": "GRCh38_GIABv3",
          "tracks": [
            {
              "trackId": "hg008t_benchmark_sv",
              "type": "LinearVariantDisplay",
              "height": 40
            },
            {
              "trackId": "HG008-T_PacBio-HiFi-Revio_20240125_116x_GRCh38-GIABv3",
              "type": "LinearAlignmentsDisplay",
              "pileup": {
                "readHeight": 1
              },
              "filter": {
                "connections": {
                  "offscreenMates": "exclude"
                }
              },
              "height": 200,
              "forceLoad": true
            }
          ]
        },
        {
          "loc": "chr13:114,348,244-114,358,244",
          "assembly": "GRCh38_GIABv3",
          "tracks": [
            {
              "trackId": "hg008t_benchmark_sv",
              "type": "LinearVariantDisplay",
              "height": 40
            },
            {
              "trackId": "HG008-T_PacBio-HiFi-Revio_20240125_116x_GRCh38-GIABv3",
              "type": "LinearAlignmentsDisplay",
              "pileup": {
                "readHeight": 1
              },
              "filter": {
                "connections": {
                  "offscreenMates": "exclude"
                }
              },
              "height": 200,
              "forceLoad": true
            }
          ]
        }
      ]
    }
  ]
}
JSON

npx @jbrowse/img breakpoint --config https://jbrowse.org/demos/cgiab/config.json \
  --spec session.json \
  --width 1800 --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": "BreakpointSplitView",
      "views": [
        {
          "loc": "chr3:139,971,414-139,981,414",
          "assembly": "GRCh38_GIABv3",
          "tracks": [
            {
              "trackId": "hg008t_benchmark_sv",
              "type": "LinearVariantDisplay",
              "height": 40
            },
            {
              "trackId": "HG008-T_PacBio-HiFi-Revio_20240125_116x_GRCh38-GIABv3",
              "type": "LinearAlignmentsDisplay",
              "pileup": {
                "readHeight": 1
              },
              "filter": {
                "connections": {
                  "offscreenMates": "exclude"
                }
              },
              "height": 200,
              "forceLoad": true
            }
          ]
        },
        {
          "loc": "chr13:114,348,244-114,358,244",
          "assembly": "GRCh38_GIABv3",
          "tracks": [
            {
              "trackId": "hg008t_benchmark_sv",
              "type": "LinearVariantDisplay",
              "height": 40
            },
            {
              "trackId": "HG008-T_PacBio-HiFi-Revio_20240125_116x_GRCh38-GIABv3",
              "type": "LinearAlignmentsDisplay",
              "pileup": {
                "readHeight": 1
              },
              "filter": {
                "connections": {
                  "offscreenMates": "exclude"
                }
              },
              "height": 200,
              "forceLoad": true
            }
          ]
        }
      ]
    }
  ]
}
JSON

cat > callouts.json <<'JSON'
[
  {
    "type": "text",
    "text": "chr3 breakend",
    "fontSize": 19,
    "color": "#1f77b4",
    "background": "#dceaf6",
    "leader": true,
    "anchor": {
      "text": "SV_20",
      "alignX": "left",
      "dx": -30
    },
    "dx": -150,
    "dy": 0
  },
  {
    "type": "text",
    "text": "chr13 breakend",
    "fontSize": 19,
    "color": "#1f77b4",
    "background": "#dceaf6",
    "leader": true,
    "anchor": {
      "text": "SV_190",
      "alignX": "left",
      "dx": -30
    },
    "dx": -150,
    "dy": 0
  }
]
JSON

npx @jbrowse/capture --instance https://jbrowse.org/code/jb2/main/ \
  --config https://jbrowse.org/demos/cgiab/config.json \
  --width 1800 --height 838 \
  --timeout 180000 \
  --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.

We read the same junction three ways:

  • In the tumor reads, each split read has one half on chr13 and one on chr3, joined by a spline. The read runs forward on chr13 into the junction, then continues on the reverse strand of chr3.
  • In the matched normal, the reads run through the locus with no split. Open HG008-N-P_PacBio-HiFi-Revio_20240125_35x_GRCh38-GIABv3 from the hosted config on the same two panels.
  • In the tumor assembly, the synteny track loaded earlier shows the junction with no reads. The C-GIAB assembly resolves both loci onto one tumor contig, named for the two chromosomes it fuses.

CUZD1: a small heterozygous deletion

Use the search (magnifying glass) button in the SV inspector to find SV_85, a heterozygous deletion of two exons of CUZD1 (NCBI Gene 50624). At about 1.8 kb, the whole deletion fits in a pileup at base level.

The ClinVar CNVs track holds submitted copy-number variants and their clinical significance, served by UCSC as a bigBed:

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

{
  "type": "FeatureTrack",
  "trackId": "hg38_clinvar_cnv_ucsc",
  "name": "ClinVar CNVs (UCSC)",
  "assemblyNames": ["GRCh38_GIABv3"],
  "adapter": {
    "type": "BigBedAdapter",
    "uri": "https://hgdownload.soe.ucsc.edu/gbdb/hg38/bbi/clinvar/clinvarCnv.bb"
  },
  "displayDefaults": {
    "displayMode": "compact",
    "filter": ["jexl:feature._varLen < 50000"]
  }
}
jbrowse add-track https://hgdownload.soe.ucsc.edu/gbdb/hg38/bbi/clinvar/clinvarCnv.bb \
  --trackId hg38_clinvar_cnv_ucsc \
  --name "ClinVar CNVs (UCSC)" \
  --assemblyNames GRCh38_GIABv3 \
  --displayDefaults '{"displayMode":"compact","filter":["jexl:feature._varLen < 50000"]}'

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": "FeatureTrack",
  "trackId": "hg38_clinvar_cnv_ucsc",
  "name": "ClinVar CNVs (UCSC)",
  "assemblyNames": ["GRCh38_GIABv3"],
  "adapter": {
    "type": "BigBedAdapter",
    "uri": "https://hgdownload.soe.ucsc.edu/gbdb/hg38/bbi/clinvar/clinvarCnv.bb"
  },
  "displayDefaults": {
    "displayMode": "compact",
    "filter": ["jexl:feature._varLen < 50000"]
  }
}

The filter keeps ClinVar CNVs under 50 kb, and none of those covers this deletion.

The SV inspector after searching for SV_85, a heterozygous CUZD1 deletion, and the linear genome view its location link opens: the <DEL> ALT allele over the ClinVar CNV and NCBI RefSeq gene tracks.
Open in JBrowse Web ↗

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 pane 1: Add → SV inspector.
    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 GRCh38_GIABv3, loaded from a bgzip-compressed FASTA (.fa.gz + .fai + .gzi).
    2. Drag the bar at the bottom edge of the view to resize it (420px here).
    3. 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.
    4. Type "SV_85" into the table's search box (the magnifier above the grid)In the SV inspector the circular view draws only the rows the search leaves, so this narrows the chords too — it does not change which regions the circle shows, which is the 'show only regions with data' checkbox beside it.
  2. Open pane 2: Add → Linear genome view.
    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 GRCh38_GIABv3, loaded from a bgzip-compressed FASTA (.fa.gz + .fai + .gzi).
    2. 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 (hg38)”.
    3. Add the next track the same way. This one needs a BigBed file (.bb).This figure uses “ClinVar CNVs (UCSC)”.
      1. Track menu → Feature height → Track sizing → Fixed feature height + autogrow track height
    4. Add the next track the same way. This one needs a bgzip-compressed, tabix-indexed VCF (.vcf.gz + .tbi).This figure uses “HG008-T V0.5 draft benchmark somatic SVs”.
      1. Right-click the feature → Highlight feature (searching for it by name in the location box leaves the same highlight behind)This figure highlights 1 feature. The spec form differs from the click in one way that matters to a figure: a highlight the user did not click also sorts its feature to a top row of the track, so it is boxed at the top of a dense lane rather than boxed several rows down.
    5. Type your region of interest into the location box and press Enter.This figure is at chr10:122,823,828-122,852,611.

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 https://hgdownload.soe.ucsc.edu/gbdb/hg38/bbi/clinvar/clinvarCnv.bb \
  --trackId hg38_clinvar_cnv_ucsc \
  --name "ClinVar CNVs (UCSC)" \
  --assemblyNames GRCh38_GIABv3 \
  --displayDefaults '{"displayMode":"compact","filter":["jexl:feature._varLen < 50000"]}'

Run these where the config.json is, or add --out <dir>, and point each uri at your own file. The config needs GRCh38_GIABv3 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/cgiab/config.json, which is what the Web button above opens.

{
  "sessionTracks": [
    {
      "type": "FeatureTrack",
      "trackId": "hg38_clinvar_cnv_ucsc",
      "name": "ClinVar CNVs (UCSC)",
      "assemblyNames": [
        "GRCh38_GIABv3"
      ],
      "adapter": {
        "type": "BigBedAdapter",
        "uri": "https://hgdownload.soe.ucsc.edu/gbdb/hg38/bbi/clinvar/clinvarCnv.bb"
      },
      "displayDefaults": {
        "displayMode": "compact",
        "filter": [
          "jexl:feature._varLen < 50000"
        ]
      }
    }
  ],
  "views": [
    {
      "type": "SvInspectorView",
      "assembly": "GRCh38_GIABv3",
      "height": 420,
      "uri": "https://jbrowse.org/genomes/GRCh38/cgiab/GRCh38_HG008-T-V0.5_somatic-stvar_PASS.draftbenchmark.vcf.gz",
      "filterText": "SV_85"
    },
    {
      "type": "LinearGenomeView",
      "assembly": "GRCh38_GIABv3",
      "loc": "chr10:122,823,828-122,852,611",
      "tracks": [
        "hg38_ncbiRefSeq_ucsc",
        {
          "trackId": "hg38_clinvar_cnv_ucsc",
          "type": "LinearBasicDisplay",
          "heightMode": "grow"
        },
        {
          "trackId": "hg008t_benchmark_sv",
          "type": "LinearVariantDisplay",
          "featureHighlights": [
            {
              "refName": "chr10",
              "name": "SV_85"
            }
          ]
        }
      ]
    }
  ]
}

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/cgiab/config.json")
app = JBrowseApp(
    assemblies=config["assemblies"],
    tracks=config.get("tracks", []) + [
        {
            "type": "FeatureTrack",
            "trackId": "hg38_clinvar_cnv_ucsc",
            "name": "ClinVar CNVs (UCSC)",
            "assemblyNames": [
                "GRCh38_GIABv3"
            ],
            "adapter": {
                "type": "BigBedAdapter",
                "uri": "https://hgdownload.soe.ucsc.edu/gbdb/hg38/bbi/clinvar/clinvarCnv.bb"
            },
            "displayDefaults": {
                "displayMode": "compact",
                "filter": [
                    "jexl:feature._varLen < 50000"
                ]
            }
        }
    ],
    views=[
        {
            "type": "SvInspectorView",
            "assembly": "GRCh38_GIABv3",
            "height": 420,
            "uri": "https://jbrowse.org/genomes/GRCh38/cgiab/GRCh38_HG008-T-V0.5_somatic-stvar_PASS.draftbenchmark.vcf.gz",
            "filterText": "SV_85"
        },
        {
            "type": "LinearGenomeView",
            "assembly": "GRCh38_GIABv3",
            "loc": "chr10:122,823,828-122,852,611",
            "tracks": [
                "hg38_ncbiRefSeq_ucsc",
                {
                    "trackId": "hg38_clinvar_cnv_ucsc",
                    "type": "LinearBasicDisplay",
                    "heightMode": "grow"
                },
                {
                    "trackId": "hg008t_benchmark_sv",
                    "type": "LinearVariantDisplay",
                    "featureHighlights": [
                        {
                            "refName": "chr10",
                            "name": "SV_85"
                        }
                    ]
                }
            ]
        }
    ],
)
app  # display the widget

Hand this to a coding agent. It rebuilds the figure above headlessly, and the session file is then the thing to edit: 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": "hg38_clinvar_cnv_ucsc",
      "name": "ClinVar CNVs (UCSC)",
      "assemblyNames": [
        "GRCh38_GIABv3"
      ],
      "adapter": {
        "type": "BigBedAdapter",
        "uri": "https://hgdownload.soe.ucsc.edu/gbdb/hg38/bbi/clinvar/clinvarCnv.bb"
      },
      "displayDefaults": {
        "displayMode": "compact",
        "filter": [
          "jexl:feature._varLen < 50000"
        ]
      }
    }
  ],
  "views": [
    {
      "type": "SvInspectorView",
      "assembly": "GRCh38_GIABv3",
      "height": 420,
      "uri": "https://jbrowse.org/genomes/GRCh38/cgiab/GRCh38_HG008-T-V0.5_somatic-stvar_PASS.draftbenchmark.vcf.gz",
      "filterText": "SV_85"
    },
    {
      "type": "LinearGenomeView",
      "assembly": "GRCh38_GIABv3",
      "loc": "chr10:122,823,828-122,852,611",
      "tracks": [
        "hg38_ncbiRefSeq_ucsc",
        {
          "trackId": "hg38_clinvar_cnv_ucsc",
          "type": "LinearBasicDisplay",
          "heightMode": "grow"
        },
        {
          "trackId": "hg008t_benchmark_sv",
          "type": "LinearVariantDisplay",
          "featureHighlights": [
            {
              "refName": "chr10",
              "name": "SV_85"
            }
          ]
        }
      ]
    }
  ]
}
JSON

cat > callouts.json <<'JSON'
[
  {
    "type": "text",
    "text": "Searching \"SV_85\" filters to one DEL (a het CUZD1 deletion)",
    "anchor": {
      "text": "chr10:122,835,344..122,837,142",
      "alignX": "left",
      "alignY": "top",
      "dx": 22,
      "dy": -40
    },
    "fontSize": 18,
    "maxWidth": 420
  },
  {
    "type": "box",
    "anchor": {
      "text": "chr10:122,835,344..122,837,142"
    }
  },
  {
    "type": "arrow",
    "fromAnchor": {
      "text": "chr10:122,835,344..122,837,142",
      "dy": 30
    },
    "anchor": {
      "view": 1,
      "trackId": "hg008t_benchmark_sv",
      "loc": "chr10:122,835,344..122,837,142",
      "fracY": 0,
      "dy": 14
    }
  },
  {
    "type": "text",
    "text": "The location link opens the region below, where SVTYPE=DEL draws as the <DEL> allele",
    "anchor": {
      "view": 1,
      "trackId": "hg008t_benchmark_sv",
      "loc": "chr10:122,835,344..122,837,142",
      "fracY": 0,
      "alignX": "right",
      "dx": 50,
      "dy": 28
    },
    "fontSize": 18,
    "maxWidth": 360
  }
]
JSON

npx @jbrowse/capture --instance https://jbrowse.org/code/jb2/main/ \
  --config https://jbrowse.org/demos/cgiab/config.json \
  --width 1500 --height 990 \
  --timeout 120000 \
  --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.

Open NCBI RefSeq genes (hg38) from the hosted config and the tumor PacBio HiFi reads, then set Read height → Compact and Sort by... → Base pair in the reads' track menu and center the deletion. Show... → Center line in the view menu helps line up the breakpoint.

Tumor HiFi reads at compact height, sorted by base pair at the deletion.
Open in JBrowse Web ↗

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 GRCh38_GIABv3, 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 GFF3 (.gff.gz + .tbi).This figure uses “NCBI RefSeq genes (hg38)”.
  3. Add the next track the same way. This one needs a bgzip-compressed, tabix-indexed VCF (.vcf.gz + .tbi).This figure uses “HG008-T V0.5 draft benchmark somatic SVs”.
  4. Add the next track the same way. This one needs a BAM file (.bam + .bai).This figure uses “HG008-T PacBio HiFi (116x, chr10 slice)”.
    1. Track menu → Read height → Compact
    2. Track menu → Sort by... → Base pairThe sort is taken at the base under the centre line, so navigate to the position you want before sorting.
  5. Type your region of interest into the location box and press Enter.This figure is at chr10:122,822,042-122,850,825.
  6. View menu → Show... → Center line (checked)

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": "AlignmentsTrack",
  "trackId": "hg008t_pacbio_chr10_deletion_slice",
  "name": "HG008-T PacBio HiFi (116x, chr10 slice)",
  "assemblyNames": [
    "GRCh38_GIABv3"
  ],
  "adapter": {
    "type": "BamAdapter",
    "bamLocation": {
      "uri": "https://jbrowse.org/demos/cgiab/HG008-T_chr10_CUZD1_deletion.bam",
      "locationType": "UriLocation"
    },
    "index": {
      "location": {
        "uri": "https://jbrowse.org/demos/cgiab/HG008-T_chr10_CUZD1_deletion.bam.bai",
        "locationType": "UriLocation"
      },
      "indexType": "BAI"
    }
  }
}'

Run these where the config.json is, or add --out <dir>, and point each uri at your own file. The config needs GRCh38_GIABv3 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/cgiab/config.json, which is what the Web button above opens.

{
  "sessionTracks": [
    {
      "type": "AlignmentsTrack",
      "trackId": "hg008t_pacbio_chr10_deletion_slice",
      "name": "HG008-T PacBio HiFi (116x, chr10 slice)",
      "assemblyNames": [
        "GRCh38_GIABv3"
      ],
      "adapter": {
        "type": "BamAdapter",
        "bamLocation": {
          "uri": "https://jbrowse.org/demos/cgiab/HG008-T_chr10_CUZD1_deletion.bam",
          "locationType": "UriLocation"
        },
        "index": {
          "location": {
            "uri": "https://jbrowse.org/demos/cgiab/HG008-T_chr10_CUZD1_deletion.bam.bai",
            "locationType": "UriLocation"
          },
          "indexType": "BAI"
        }
      }
    }
  ],
  "views": [
    {
      "type": "LinearGenomeView",
      "assembly": "GRCh38_GIABv3",
      "loc": "chr10:122,822,042-122,850,825",
      "showCenterLine": true,
      "tracks": [
        "hg38_ncbiRefSeq_ucsc",
        "hg008t_benchmark_sv",
        {
          "trackId": "hg008t_pacbio_chr10_deletion_slice",
          "height": 300,
          "pileup": {
            "readHeight": 3
          },
          "sort": {
            "type": "basePair",
            "pos": 122836434,
            "refName": "chr10"
          }
        }
      ]
    }
  ]
}

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/cgiab/config.json")
app = JBrowseApp(
    assemblies=config["assemblies"],
    tracks=config.get("tracks", []) + [
        {
            "type": "AlignmentsTrack",
            "trackId": "hg008t_pacbio_chr10_deletion_slice",
            "name": "HG008-T PacBio HiFi (116x, chr10 slice)",
            "assemblyNames": [
                "GRCh38_GIABv3"
            ],
            "adapter": {
                "type": "BamAdapter",
                "bamLocation": {
                    "uri": "https://jbrowse.org/demos/cgiab/HG008-T_chr10_CUZD1_deletion.bam",
                    "locationType": "UriLocation"
                },
                "index": {
                    "location": {
                        "uri": "https://jbrowse.org/demos/cgiab/HG008-T_chr10_CUZD1_deletion.bam.bai",
                        "locationType": "UriLocation"
                    },
                    "indexType": "BAI"
                }
            }
        }
    ],
    views=[
        {
            "type": "LinearGenomeView",
            "assembly": "GRCh38_GIABv3",
            "loc": "chr10:122,822,042-122,850,825",
            "showCenterLine": True,
            "tracks": [
                "hg38_ncbiRefSeq_ucsc",
                "hg008t_benchmark_sv",
                {
                    "trackId": "hg008t_pacbio_chr10_deletion_slice",
                    "height": 300,
                    "pileup": {
                        "readHeight": 3
                    },
                    "sort": {
                        "type": "basePair",
                        "pos": 122836434,
                        "refName": "chr10"
                    }
                }
            ]
        }
    ],
)
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": "AlignmentsTrack",
    "trackId": "hg008t_pacbio_chr10_deletion_slice",
    "name": "HG008-T PacBio HiFi (116x, chr10 slice)",
    "assemblyNames": [
      "GRCh38_GIABv3"
    ],
    "adapter": {
      "type": "BamAdapter",
      "bamLocation": {
        "uri": "https://jbrowse.org/demos/cgiab/HG008-T_chr10_CUZD1_deletion.bam",
        "locationType": "UriLocation"
      },
      "index": {
        "location": {
          "uri": "https://jbrowse.org/demos/cgiab/HG008-T_chr10_CUZD1_deletion.bam.bai",
          "locationType": "UriLocation"
        },
        "indexType": "BAI"
      }
    }
  }
]
JSON

npx @jbrowse/img --config https://jbrowse.org/demos/cgiab/config.json \
  --tracks tracks.json \
  --assembly GRCh38_GIABv3 --loc chr10:122,822,042-122,850,825 \
  --track hg38_ncbiRefSeq_ucsc \
  --track hg008t_benchmark_sv \
  --track hg008t_pacbio_chr10_deletion_slice '{"height":300,"pileup":{"readHeight":3},"sort":{"type":"basePair","pos":122836434,"refName":"chr10"}}' \
  --width 1500 --out figure.svg

It has no flag for this figure's showCenterLine, 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.

cat > session.json <<'JSON'
{
  "sessionTracks": [
    {
      "type": "AlignmentsTrack",
      "trackId": "hg008t_pacbio_chr10_deletion_slice",
      "name": "HG008-T PacBio HiFi (116x, chr10 slice)",
      "assemblyNames": [
        "GRCh38_GIABv3"
      ],
      "adapter": {
        "type": "BamAdapter",
        "bamLocation": {
          "uri": "https://jbrowse.org/demos/cgiab/HG008-T_chr10_CUZD1_deletion.bam",
          "locationType": "UriLocation"
        },
        "index": {
          "location": {
            "uri": "https://jbrowse.org/demos/cgiab/HG008-T_chr10_CUZD1_deletion.bam.bai",
            "locationType": "UriLocation"
          },
          "indexType": "BAI"
        }
      }
    }
  ],
  "views": [
    {
      "type": "LinearGenomeView",
      "assembly": "GRCh38_GIABv3",
      "loc": "chr10:122,822,042-122,850,825",
      "showCenterLine": true,
      "tracks": [
        "hg38_ncbiRefSeq_ucsc",
        "hg008t_benchmark_sv",
        {
          "trackId": "hg008t_pacbio_chr10_deletion_slice",
          "height": 300,
          "pileup": {
            "readHeight": 3
          },
          "sort": {
            "type": "basePair",
            "pos": 122836434,
            "refName": "chr10"
          }
        }
      ]
    }
  ]
}
JSON

npx @jbrowse/capture --instance https://jbrowse.org/code/jb2/main/ \
  --config https://jbrowse.org/demos/cgiab/config.json \
  --width 1500 --height 800 \
  --spec 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.

Dotplot and synteny views of the tumor assembly against GRCh38

Add → Dotplot view, set the tumor assembly as one axis and GRCh38 as the other, and pick the matching synteny track.

HG008-T v3.2's scaffold names end in _hap1 or _hap2, so one plot stacks both haplotypes and doubles every diagonal. In the import form, tick Plot only certain chromosomes and type *_hap1 into the chromosomes box of the HG008T_v3.2 axis, then *_hap2 in a second view, for a plain assembly-vs-reference diagonal per haplotype.

HG008-T's two haplotypes (y) against GRCh38 (x) as dotplots, hap1 left and hap2 right.
Open in JBrowse Web ↗

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. Pane 1
    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 has GRCh38_GIABv3 on X and HG008T_v3.2 on Y.
    2. Open the view: Add → Dotplot view, and set both axes to those assemblies in the import form.
    3. Point the import form at your own file: use the track panel under the two axis selectors, 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 both axes itself.This figure uses “HG008T v3.2”.
    4. Click Launch.
    5. Click the view's title in its header and enter "HG008-T v3.2 hap1 vs GRCh38"
    6. Dotplot header → the ⋮ menu → Re-order chromosomes...Reorders and flips the vertical axis so the best-hit blocks line up on a diagonal. The spec runs it once as the view opens; the menu item is the same thing on demand.
    7. Drag the bar at the bottom edge of the view to resize it (640px here).
  2. Pane 2
    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 has GRCh38_GIABv3 on X and HG008T_v3.2 on Y.
    2. Open the view: Add → Dotplot view, and set both axes to those assemblies in the import form.
    3. Point the import form at your own file: use the track panel under the two axis selectors, 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 both axes itself.This figure uses “HG008T v3.2”.
    4. Click Launch.
    5. Click the view's title in its header and enter "HG008-T v3.2 hap2 vs GRCh38"
    6. Dotplot header → the ⋮ menu → Re-order chromosomes...Reorders and flips the vertical axis so the best-hit blocks line up on a diagonal. The spec runs it once as the view opens; the menu item is the same thing on demand.
    7. Drag the bar at the bottom edge of the view to resize it (640px here).

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

{
  "views": [
    {
      "type": "DotplotView",
      "displayName": "HG008-T v3.2 hap1 vs GRCh38",
      "views": [
        {
          "assembly": "GRCh38_GIABv3"
        },
        {
          "assembly": "HG008T_v3.2",
          "displayedRegionNames": [
            "*_hap1"
          ]
        }
      ],
      "tracks": [
        "HG008T_v3.2_pif"
      ],
      "autoDiagonalize": true,
      "height": 640
    },
    {
      "type": "DotplotView",
      "displayName": "HG008-T v3.2 hap2 vs GRCh38",
      "views": [
        {
          "assembly": "GRCh38_GIABv3"
        },
        {
          "assembly": "HG008T_v3.2",
          "displayedRegionNames": [
            "*_hap2"
          ]
        }
      ],
      "tracks": [
        "HG008T_v3.2_pif"
      ],
      "autoDiagonalize": true,
      "height": 640
    }
  ],
  "layout": {
    "direction": "horizontal",
    "children": [
      {
        "views": [
          0
        ],
        "size": 50
      },
      {
        "views": [
          1
        ],
        "size": 50
      }
    ]
  }
}

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/cgiab/config.json")
app = JBrowseApp(
    assemblies=config["assemblies"],
    tracks=config.get("tracks", []),
    views=[
        {
            "type": "DotplotView",
            "displayName": "HG008-T v3.2 hap1 vs GRCh38",
            "views": [
                {
                    "assembly": "GRCh38_GIABv3"
                },
                {
                    "assembly": "HG008T_v3.2",
                    "displayedRegionNames": [
                        "*_hap1"
                    ]
                }
            ],
            "tracks": [
                "HG008T_v3.2_pif"
            ],
            "autoDiagonalize": True,
            "height": 640
        },
        {
            "type": "DotplotView",
            "displayName": "HG008-T v3.2 hap2 vs GRCh38",
            "views": [
                {
                    "assembly": "GRCh38_GIABv3"
                },
                {
                    "assembly": "HG008T_v3.2",
                    "displayedRegionNames": [
                        "*_hap2"
                    ]
                }
            ],
            "tracks": [
                "HG008T_v3.2_pif"
            ],
            "autoDiagonalize": True,
            "height": 640
        }
    ],
)
app  # display the widget

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

cat > session.json <<'JSON'
{
  "views": [
    {
      "type": "DotplotView",
      "displayName": "HG008-T v3.2 hap1 vs GRCh38",
      "views": [
        {
          "assembly": "GRCh38_GIABv3"
        },
        {
          "assembly": "HG008T_v3.2",
          "displayedRegionNames": [
            "*_hap1"
          ]
        }
      ],
      "tracks": [
        "HG008T_v3.2_pif"
      ],
      "autoDiagonalize": true,
      "height": 640
    },
    {
      "type": "DotplotView",
      "displayName": "HG008-T v3.2 hap2 vs GRCh38",
      "views": [
        {
          "assembly": "GRCh38_GIABv3"
        },
        {
          "assembly": "HG008T_v3.2",
          "displayedRegionNames": [
            "*_hap2"
          ]
        }
      ],
      "tracks": [
        "HG008T_v3.2_pif"
      ],
      "autoDiagonalize": true,
      "height": 640
    }
  ],
  "layout": {
    "direction": "horizontal",
    "children": [
      {
        "views": [
          0
        ],
        "size": 50
      },
      {
        "views": [
          1
        ],
        "size": 50
      }
    ]
  }
}
JSON

cat > callouts.json <<'JSON'
[
  {
    "type": "text",
    "text": "chr3/chr13 fusion",
    "leader": true,
    "anchor": {
      "view": 0,
      "hLoc": "chr13",
      "vLoc": "chr3_chr13_hap1"
    },
    "dx": 40,
    "dy": 80
  },
  {
    "type": "text",
    "text": "chr13 intact",
    "leader": true,
    "anchor": {
      "view": 1,
      "hLoc": "chr13",
      "vLoc": "chr13_hap2"
    },
    "dx": 40,
    "dy": 80
  }
]
JSON

npx @jbrowse/capture --instance https://jbrowse.org/code/jb2/main/ \
  --config https://jbrowse.org/demos/cgiab/config.json \
  --width 1800 --height 820 \
  --timeout 90000 \
  --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.

Drag over a region and take Launch → Linear synteny view, keeping HG008T_v3.2 vs GRCh38_GIABv3 (HG008T v3.2 in the hosted config) as the synteny track, then enter chr13 chr3 in the GRCh38 search box.

The breakpoint split view's two reference windows with tumor reads grouped by split read, above the fused scaffold. A curve joins the two halves of each split read.
Open in JBrowse Web ↗

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 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: GRCh38_GIABv3, HG008T_v3.2.
  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 “HG008T v3.2”.
  4. Click Launch.
  5. Synteny display settings (the sliders button in the view header) → Curved lines (checked)
  6. Drag the bar below a synteny level to resize it.This figure's level is 150px tall.
  7. Synteny display settings (the sliders button in the view header) → Opacity → drag to 0.35Lower values let dense overlapping ribbons show through each other.
  8. Synteny display settings (the sliders button in the view header) → Off-screen mates (unchecked)On by default: a locus syntenic to a contig the facing panel is not showing draws no ribbon, so without the marks it looks exactly like a locus syntenic to nothing.
  9. Row 1 (GRCh38_GIABv3)
    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 VCF (.vcf.gz + .tbi).This figure uses “HG008-T V0.5 draft benchmark somatic SVs”.
    2. Add the next track the same way. This one needs a BAM file (.bam + .bai).This figure uses “HG008-T_PacBio-HiFi-Revio_20240125_116x_GRCh38-GIABv3”.
      1. Track menu → Read height → Custom... → 2px
      2. Track menu → Read connections → Off-screen mate connections → Hide off-screen mate connectionsThe row stays greyed out until an arc or read-cloud overlay, or the curved connectors, are on.
      3. 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. Track menu → Read connections → View as pairs / link supplementary alignments (checked)
      5. Track menu → Group by... → Split read (SA tag)
      6. Track menu → Color by... → Paired end → Pair orientation
      7. Track menu → Show... → Legend (checked)
      8. Track menu → Read connections → Read arcs
      9. Drag the handle at the edge of the arc band to resize it (70px here).Its tooltip reads "Drag to resize arcs area"; there is no menu entry for the height.
    3. Type your region of interest into the location box and press Enter.This figure is at chr13:114,348,244-114,358,244 chr3:139,971,415-139,981,415.
    4. 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 (HG008T_v3.2)
    1. Type your region of interest into the location box and press Enter.This figure is at chr3_chr13_hap1:106,646,329-106,656,329.
    2. View menu → Show... → No tracks active button (unchecked)
    3. 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/cgiab/config.json, which is what the Web button above opens.

{
  "views": [
    {
      "type": "LinearSyntenyView",
      "drawCurves": true,
      "levelHeights": [
        150
      ],
      "opacity": 0.35,
      "showOffscreenMates": false,
      "tracks": [
        [
          "HG008T_v3.2_pif"
        ]
      ],
      "views": [
        {
          "loc": "chr13:114,348,244-114,358,244 chr3:139,971,415-139,981,415",
          "assembly": "GRCh38_GIABv3",
          "tracks": [
            {
              "trackId": "hg008t_benchmark_sv",
              "type": "LinearVariantDisplay",
              "height": 40
            },
            {
              "trackId": "HG008-T_PacBio-HiFi-Revio_20240125_116x_GRCh38-GIABv3",
              "type": "LinearAlignmentsDisplay",
              "pileup": {
                "readHeight": 2
              },
              "filter": {
                "connections": {
                  "offscreenMates": "exclude"
                }
              },
              "height": 690,
              "forceLoad": true,
              "unit": "chain",
              "facet": "split",
              "color": {
                "field": "pairOrientation"
              },
              "showLegend": true,
              "readConnections": {
                "show": true,
                "height": 70
              }
            }
          ],
          "highlight": [
            {
              "assemblyName": "GRCh38_GIABv3",
              "refName": "chr13",
              "start": 114353224,
              "end": 114353264,
              "color": "rgba(31,119,180,0.45)"
            },
            {
              "assemblyName": "GRCh38_GIABv3",
              "refName": "chr3",
              "start": 139976395,
              "end": 139976435,
              "color": "rgba(31,119,180,0.45)"
            }
          ]
        },
        {
          "loc": "chr3_chr13_hap1:106,646,329-106,656,329",
          "assembly": "HG008T_v3.2",
          "hideNoTracksActive": true,
          "highlight": [
            {
              "assemblyName": "HG008T_v3.2",
              "refName": "chr3_chr13_hap1",
              "start": 106651319,
              "end": 106651339,
              "color": "rgba(31,119,180,0.45)"
            }
          ]
        }
      ]
    }
  ]
}

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/cgiab/config.json")
app = JBrowseApp(
    assemblies=config["assemblies"],
    tracks=config.get("tracks", []),
    views=[
        {
            "type": "LinearSyntenyView",
            "drawCurves": True,
            "levelHeights": [
                150
            ],
            "opacity": 0.35,
            "showOffscreenMates": False,
            "tracks": [
                [
                    "HG008T_v3.2_pif"
                ]
            ],
            "views": [
                {
                    "loc": "chr13:114,348,244-114,358,244 chr3:139,971,415-139,981,415",
                    "assembly": "GRCh38_GIABv3",
                    "tracks": [
                        {
                            "trackId": "hg008t_benchmark_sv",
                            "type": "LinearVariantDisplay",
                            "height": 40
                        },
                        {
                            "trackId": "HG008-T_PacBio-HiFi-Revio_20240125_116x_GRCh38-GIABv3",
                            "type": "LinearAlignmentsDisplay",
                            "pileup": {
                                "readHeight": 2
                            },
                            "filter": {
                                "connections": {
                                    "offscreenMates": "exclude"
                                }
                            },
                            "height": 690,
                            "forceLoad": True,
                            "unit": "chain",
                            "facet": "split",
                            "color": {
                                "field": "pairOrientation"
                            },
                            "showLegend": True,
                            "readConnections": {
                                "show": True,
                                "height": 70
                            }
                        }
                    ],
                    "highlight": [
                        {
                            "assemblyName": "GRCh38_GIABv3",
                            "refName": "chr13",
                            "start": 114353224,
                            "end": 114353264,
                            "color": "rgba(31,119,180,0.45)"
                        },
                        {
                            "assemblyName": "GRCh38_GIABv3",
                            "refName": "chr3",
                            "start": 139976395,
                            "end": 139976435,
                            "color": "rgba(31,119,180,0.45)"
                        }
                    ]
                },
                {
                    "loc": "chr3_chr13_hap1:106,646,329-106,656,329",
                    "assembly": "HG008T_v3.2",
                    "hideNoTracksActive": True,
                    "highlight": [
                        {
                            "assemblyName": "HG008T_v3.2",
                            "refName": "chr3_chr13_hap1",
                            "start": 106651319,
                            "end": 106651339,
                            "color": "rgba(31,119,180,0.45)"
                        }
                    ]
                }
            ]
        }
    ],
)
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": "LinearSyntenyView",
      "drawCurves": true,
      "levelHeights": [
        150
      ],
      "opacity": 0.35,
      "showOffscreenMates": false,
      "tracks": [
        [
          "HG008T_v3.2_pif"
        ]
      ],
      "views": [
        {
          "loc": "chr13:114,348,244-114,358,244 chr3:139,971,415-139,981,415",
          "assembly": "GRCh38_GIABv3",
          "tracks": [
            {
              "trackId": "hg008t_benchmark_sv",
              "type": "LinearVariantDisplay",
              "height": 40
            },
            {
              "trackId": "HG008-T_PacBio-HiFi-Revio_20240125_116x_GRCh38-GIABv3",
              "type": "LinearAlignmentsDisplay",
              "pileup": {
                "readHeight": 2
              },
              "filter": {
                "connections": {
                  "offscreenMates": "exclude"
                }
              },
              "height": 690,
              "forceLoad": true,
              "unit": "chain",
              "facet": "split",
              "color": {
                "field": "pairOrientation"
              },
              "showLegend": true,
              "readConnections": {
                "show": true,
                "height": 70
              }
            }
          ],
          "highlight": [
            {
              "assemblyName": "GRCh38_GIABv3",
              "refName": "chr13",
              "start": 114353224,
              "end": 114353264,
              "color": "rgba(31,119,180,0.45)"
            },
            {
              "assemblyName": "GRCh38_GIABv3",
              "refName": "chr3",
              "start": 139976395,
              "end": 139976435,
              "color": "rgba(31,119,180,0.45)"
            }
          ]
        },
        {
          "loc": "chr3_chr13_hap1:106,646,329-106,656,329",
          "assembly": "HG008T_v3.2",
          "hideNoTracksActive": true,
          "highlight": [
            {
              "assemblyName": "HG008T_v3.2",
              "refName": "chr3_chr13_hap1",
              "start": 106651319,
              "end": 106651339,
              "color": "rgba(31,119,180,0.45)"
            }
          ]
        }
      ]
    }
  ]
}
JSON

npx @jbrowse/img synteny --config https://jbrowse.org/demos/cgiab/config.json \
  --spec session.json \
  --width 1800 --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": "LinearSyntenyView",
      "drawCurves": true,
      "levelHeights": [
        150
      ],
      "opacity": 0.35,
      "showOffscreenMates": false,
      "tracks": [
        [
          "HG008T_v3.2_pif"
        ]
      ],
      "views": [
        {
          "loc": "chr13:114,348,244-114,358,244 chr3:139,971,415-139,981,415",
          "assembly": "GRCh38_GIABv3",
          "tracks": [
            {
              "trackId": "hg008t_benchmark_sv",
              "type": "LinearVariantDisplay",
              "height": 40
            },
            {
              "trackId": "HG008-T_PacBio-HiFi-Revio_20240125_116x_GRCh38-GIABv3",
              "type": "LinearAlignmentsDisplay",
              "pileup": {
                "readHeight": 2
              },
              "filter": {
                "connections": {
                  "offscreenMates": "exclude"
                }
              },
              "height": 690,
              "forceLoad": true,
              "unit": "chain",
              "facet": "split",
              "color": {
                "field": "pairOrientation"
              },
              "showLegend": true,
              "readConnections": {
                "show": true,
                "height": 70
              }
            }
          ],
          "highlight": [
            {
              "assemblyName": "GRCh38_GIABv3",
              "refName": "chr13",
              "start": 114353224,
              "end": 114353264,
              "color": "rgba(31,119,180,0.45)"
            },
            {
              "assemblyName": "GRCh38_GIABv3",
              "refName": "chr3",
              "start": 139976395,
              "end": 139976435,
              "color": "rgba(31,119,180,0.45)"
            }
          ]
        },
        {
          "loc": "chr3_chr13_hap1:106,646,329-106,656,329",
          "assembly": "HG008T_v3.2",
          "hideNoTracksActive": true,
          "highlight": [
            {
              "assemblyName": "HG008T_v3.2",
              "refName": "chr3_chr13_hap1",
              "start": 106651319,
              "end": 106651339,
              "color": "rgba(31,119,180,0.45)"
            }
          ]
        }
      ]
    }
  ]
}
JSON

cat > callouts.json <<'JSON'
[
  {
    "type": "text",
    "text": "hap1",
    "fontSize": 19,
    "anchor": {
      "selector": "[data-testid=\"refLabel-prefix\"]",
      "view": [
        0,
        1
      ],
      "alignX": "left",
      "alignY": "bottom",
      "dx": 4,
      "dy": 26
    }
  },
  {
    "type": "text",
    "text": "chr13 breakend",
    "fontSize": 19,
    "color": "#1f77b4",
    "background": "#dceaf6",
    "leader": true,
    "anchor": {
      "selector": "[data-testid=\"highlight-band\"]",
      "view": [
        0,
        0
      ],
      "alignY": "top"
    },
    "dx": 190,
    "dy": 70
  },
  {
    "type": "text",
    "text": "chr3 breakend",
    "fontSize": 19,
    "color": "#1f77b4",
    "background": "#dceaf6",
    "leader": true,
    "anchor": {
      "selector": "[data-testid=\"highlight-band\"] ~ [data-testid=\"highlight-band\"]",
      "view": [
        0,
        0
      ],
      "alignY": "top"
    },
    "dx": 140,
    "dy": 70
  },
  {
    "type": "text",
    "text": "junction",
    "fontSize": 19,
    "color": "#1f77b4",
    "background": "#dceaf6",
    "leader": true,
    "anchor": {
      "selector": "[data-testid=\"highlight-band\"]",
      "view": [
        0,
        1
      ],
      "alignY": "center"
    },
    "dx": 170,
    "dy": 8
  },
  {
    "type": "text",
    "text": "SV calls",
    "fontSize": 19,
    "anchor": {
      "text": "draft benchmark somatic SVs",
      "alignX": "left",
      "alignY": "bottom",
      "dx": -50,
      "dy": 22
    }
  },
  {
    "type": "text",
    "text": "aggregate read links",
    "fontSize": 19,
    "anchor": {
      "text": "HG008-T_PacBio-HiFi-Revio_20240125_116x_GRCh38-GIABv3",
      "alignX": "left",
      "alignY": "bottom",
      "dx": -50,
      "dy": 92
    }
  },
  {
    "type": "text",
    "text": "split reads",
    "fontSize": 19,
    "anchor": {
      "text": "HG008-T_PacBio-HiFi-Revio_20240125_116x_GRCh38-GIABv3",
      "alignX": "left",
      "alignY": "bottom",
      "dx": -50,
      "dy": 250
    }
  },
  {
    "type": "text",
    "text": "unsplit reads",
    "fontSize": 19,
    "anchor": {
      "text": "HG008-T_PacBio-HiFi-Revio_20240125_116x_GRCh38-GIABv3",
      "alignX": "left",
      "alignY": "bottom",
      "dx": -50,
      "dy": 610
    }
  }
]
JSON

npx @jbrowse/capture --instance https://jbrowse.org/code/jb2/main/ \
  --config https://jbrowse.org/demos/cgiab/config.json \
  --width 1800 --height 1220 \
  --timeout 180000 \
  --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.

Add row in the import form gives each haplotype a separate row: hap2, GRCh38, hap1, with ribbons between each adjacent pair.

A synteny view of hap2, GRCh38 chr13 and chr3, and the fused chr3_chr13_hap1 scaffold.
Open in JBrowse Web ↗

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 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: HG008T_v3.2, GRCh38_GIABv3, HG008T_v3.2.
  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 “HG008T v3.2”.
  4. Click Launch.
  5. Synteny display settings (the sliders button in the view header) → Curved lines (checked)
  6. Drag the bar below a synteny level to resize it.This figure's 2 levels are 200, 200px tall.
  7. Synteny display settings (the sliders button in the view header) → Min length → drag to 100,000bpHides alignments shorter than this, which is what clears the hairball of short spurious chains at whole-genome zoom.
  8. Synteny display settings (the sliders button in the view header) → Opacity → drag to 0.35Lower values let dense overlapping ribbons show through each other.
  9. Synteny display settings (the sliders button in the view header) → Off-screen mates (unchecked)On by default: a locus syntenic to a contig the facing panel is not showing draws no ribbon, so without the marks it looks exactly like a locus syntenic to nothing.
  10. Row 1 (HG008T_v3.2)
    1. Type your region of interest into the location box and press Enter.This figure is at chr13_hap2:1-99565785 chr3_chr6_chr11_hap2:1-196000000.
    2. View menu → Show... → No tracks active button (unchecked)
  11. Row 2 (GRCh38_GIABv3)
    1. Type your region of interest into the location box and press Enter.This figure is at chr13:1-114364328 chr3:1-198295559.
    2. View menu → Show... → No tracks active button (unchecked)
    3. 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.
  12. Row 3 (HG008T_v3.2)
    1. Type your region of interest into the location box and press Enter.This figure is at chr3_chr13_hap1:1-212897834.
    2. View menu → Show... → No tracks active button (unchecked)
    3. 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/cgiab/config.json, which is what the Web button above opens.

{
  "views": [
    {
      "type": "LinearSyntenyView",
      "drawCurves": true,
      "levelHeights": [
        200,
        200
      ],
      "minAlignmentLength": 100000,
      "opacity": 0.35,
      "showOffscreenMates": false,
      "tracks": [
        "HG008T_v3.2_pif"
      ],
      "views": [
        {
          "loc": "chr13_hap2:1-99565785 chr3_chr6_chr11_hap2:1-196000000",
          "assembly": "HG008T_v3.2",
          "hideNoTracksActive": true
        },
        {
          "loc": "chr13:1-114364328 chr3:1-198295559",
          "assembly": "GRCh38_GIABv3",
          "hideNoTracksActive": true,
          "highlight": [
            {
              "assemblyName": "GRCh38_GIABv3",
              "refName": "chr13",
              "start": 113964328,
              "end": 114364328,
              "color": "rgba(31,119,180,0.45)"
            },
            {
              "assemblyName": "GRCh38_GIABv3",
              "refName": "chr3",
              "start": 139776414,
              "end": 140176414,
              "color": "rgba(31,119,180,0.45)"
            }
          ]
        },
        {
          "loc": "chr3_chr13_hap1:1-212897834",
          "assembly": "HG008T_v3.2",
          "hideNoTracksActive": true,
          "highlight": [
            {
              "assemblyName": "HG008T_v3.2",
              "refName": "chr3_chr13_hap1",
              "start": 106501329,
              "end": 106801329,
              "color": "rgba(31,119,180,0.45)"
            }
          ]
        }
      ]
    }
  ]
}

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/cgiab/config.json")
app = JBrowseApp(
    assemblies=config["assemblies"],
    tracks=config.get("tracks", []),
    views=[
        {
            "type": "LinearSyntenyView",
            "drawCurves": True,
            "levelHeights": [
                200,
                200
            ],
            "minAlignmentLength": 100000,
            "opacity": 0.35,
            "showOffscreenMates": False,
            "tracks": [
                "HG008T_v3.2_pif"
            ],
            "views": [
                {
                    "loc": "chr13_hap2:1-99565785 chr3_chr6_chr11_hap2:1-196000000",
                    "assembly": "HG008T_v3.2",
                    "hideNoTracksActive": True
                },
                {
                    "loc": "chr13:1-114364328 chr3:1-198295559",
                    "assembly": "GRCh38_GIABv3",
                    "hideNoTracksActive": True,
                    "highlight": [
                        {
                            "assemblyName": "GRCh38_GIABv3",
                            "refName": "chr13",
                            "start": 113964328,
                            "end": 114364328,
                            "color": "rgba(31,119,180,0.45)"
                        },
                        {
                            "assemblyName": "GRCh38_GIABv3",
                            "refName": "chr3",
                            "start": 139776414,
                            "end": 140176414,
                            "color": "rgba(31,119,180,0.45)"
                        }
                    ]
                },
                {
                    "loc": "chr3_chr13_hap1:1-212897834",
                    "assembly": "HG008T_v3.2",
                    "hideNoTracksActive": True,
                    "highlight": [
                        {
                            "assemblyName": "HG008T_v3.2",
                            "refName": "chr3_chr13_hap1",
                            "start": 106501329,
                            "end": 106801329,
                            "color": "rgba(31,119,180,0.45)"
                        }
                    ]
                }
            ]
        }
    ],
)
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": "LinearSyntenyView",
      "drawCurves": true,
      "levelHeights": [
        200,
        200
      ],
      "minAlignmentLength": 100000,
      "opacity": 0.35,
      "showOffscreenMates": false,
      "tracks": [
        "HG008T_v3.2_pif"
      ],
      "views": [
        {
          "loc": "chr13_hap2:1-99565785 chr3_chr6_chr11_hap2:1-196000000",
          "assembly": "HG008T_v3.2",
          "hideNoTracksActive": true
        },
        {
          "loc": "chr13:1-114364328 chr3:1-198295559",
          "assembly": "GRCh38_GIABv3",
          "hideNoTracksActive": true,
          "highlight": [
            {
              "assemblyName": "GRCh38_GIABv3",
              "refName": "chr13",
              "start": 113964328,
              "end": 114364328,
              "color": "rgba(31,119,180,0.45)"
            },
            {
              "assemblyName": "GRCh38_GIABv3",
              "refName": "chr3",
              "start": 139776414,
              "end": 140176414,
              "color": "rgba(31,119,180,0.45)"
            }
          ]
        },
        {
          "loc": "chr3_chr13_hap1:1-212897834",
          "assembly": "HG008T_v3.2",
          "hideNoTracksActive": true,
          "highlight": [
            {
              "assemblyName": "HG008T_v3.2",
              "refName": "chr3_chr13_hap1",
              "start": 106501329,
              "end": 106801329,
              "color": "rgba(31,119,180,0.45)"
            }
          ]
        }
      ]
    }
  ]
}
JSON

npx @jbrowse/img synteny --config https://jbrowse.org/demos/cgiab/config.json \
  --spec session.json \
  --width 1800 --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": "LinearSyntenyView",
      "drawCurves": true,
      "levelHeights": [
        200,
        200
      ],
      "minAlignmentLength": 100000,
      "opacity": 0.35,
      "showOffscreenMates": false,
      "tracks": [
        "HG008T_v3.2_pif"
      ],
      "views": [
        {
          "loc": "chr13_hap2:1-99565785 chr3_chr6_chr11_hap2:1-196000000",
          "assembly": "HG008T_v3.2",
          "hideNoTracksActive": true
        },
        {
          "loc": "chr13:1-114364328 chr3:1-198295559",
          "assembly": "GRCh38_GIABv3",
          "hideNoTracksActive": true,
          "highlight": [
            {
              "assemblyName": "GRCh38_GIABv3",
              "refName": "chr13",
              "start": 113964328,
              "end": 114364328,
              "color": "rgba(31,119,180,0.45)"
            },
            {
              "assemblyName": "GRCh38_GIABv3",
              "refName": "chr3",
              "start": 139776414,
              "end": 140176414,
              "color": "rgba(31,119,180,0.45)"
            }
          ]
        },
        {
          "loc": "chr3_chr13_hap1:1-212897834",
          "assembly": "HG008T_v3.2",
          "hideNoTracksActive": true,
          "highlight": [
            {
              "assemblyName": "HG008T_v3.2",
              "refName": "chr3_chr13_hap1",
              "start": 106501329,
              "end": 106801329,
              "color": "rgba(31,119,180,0.45)"
            }
          ]
        }
      ]
    }
  ]
}
JSON

cat > callouts.json <<'JSON'
[
  {
    "type": "text",
    "text": "hap2",
    "fontSize": 19,
    "anchor": {
      "selector": "[data-testid=\"refLabel-prefix\"]",
      "view": [
        0,
        0
      ],
      "alignX": "left",
      "alignY": "bottom",
      "dx": 4,
      "dy": 26
    }
  },
  {
    "type": "text",
    "text": "GRCh38",
    "fontSize": 19,
    "anchor": {
      "selector": "[data-testid=\"refLabel-prefix\"]",
      "view": [
        0,
        1
      ],
      "alignX": "left",
      "alignY": "bottom",
      "dx": 4,
      "dy": 26
    }
  },
  {
    "type": "text",
    "text": "hap1",
    "fontSize": 19,
    "anchor": {
      "selector": "[data-testid=\"refLabel-prefix\"]",
      "view": [
        0,
        2
      ],
      "alignX": "left",
      "alignY": "bottom",
      "dx": 4,
      "dy": 26
    }
  },
  {
    "type": "text",
    "text": "chr13 breakend",
    "fontSize": 19,
    "color": "#1f77b4",
    "background": "#dceaf6",
    "leader": true,
    "anchor": {
      "selector": "[data-testid=\"highlight-band\"]",
      "view": [
        0,
        1
      ],
      "alignY": "top"
    },
    "dx": -150,
    "dy": 40
  },
  {
    "type": "text",
    "text": "chr3 breakend",
    "fontSize": 19,
    "color": "#1f77b4",
    "background": "#dceaf6",
    "leader": true,
    "anchor": {
      "selector": "[data-testid=\"highlight-band\"] ~ [data-testid=\"highlight-band\"]",
      "view": [
        0,
        1
      ],
      "alignY": "top"
    },
    "dx": -150,
    "dy": 40
  },
  {
    "type": "text",
    "text": "junction",
    "fontSize": 19,
    "color": "#1f77b4",
    "background": "#dceaf6",
    "leader": true,
    "anchor": {
      "selector": "[data-testid=\"highlight-band\"]",
      "view": [
        0,
        2
      ],
      "alignY": "center"
    },
    "dx": 170,
    "dy": 8
  }
]
JSON

npx @jbrowse/capture --instance https://jbrowse.org/code/jb2/main/ \
  --config https://jbrowse.org/demos/cgiab/config.json \
  --width 1800 --height 806 \
  --timeout 180000 \
  --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.

The dotplot view guide and the linear synteny view guide cover these views.

Reproduce it end to end

build_sv_visualization_cgiab.sh runs the data preparation above in one shot. The script:

  1. Fetches the C-GIAB GRCh38 build and the V0.5 benchmark calls.
  2. Runs the CRAM and minimap2 steps above, and the coverage, HiFiCNV and BAF steps of part 2.
  3. Downloads JBrowse and writes a config.json with all of it loaded beside the published Wakhan segments.
curl -fO https://raw.githubusercontent.com/GMOD/jbrowse-components/main/scripts/build_sv_visualization_cgiab.sh
bash build_sv_visualization_cgiab.sh   # builds ./cgiab_build/jbrowse2
npx --yes serve cgiab_build/jbrowse2

The script downloads over 200 GB and takes hours.

See also

Citations