Release v3.3.0

[cmdcolin]

Hello all,

This release adds a significant update to the multi-variant renderer that allows it to be used for visualizing structural variants. Previously, all variants >10bp were filtered out, with the idea that overlapping variants are too difficult to interpret. JBrowse will now actually draw long, even overlapping, structural variants using the multi-sample variant display mode.

Figure: Screenshot showing many SV calls over a 5Mbp+ region from the 3,202 human samples from the 1000 genomes project, with a large "inversion" variant showing the shaded triangles. The right side panel shows the feature details for this inversion variant showing the new genotype frequency panel, indicating about 47% of samples have a 'heterozygous' inversion call here.

We hope that you enjoy these new features! The visualizations may be visually complex but we hope it can be a magnifying glass to see the true complexity of your data. Feel free to let us know if you have any feedback!

Other notable changes, mostly internal

• Upgrading dependencies: @mui/material v6->v7 and @mui/x-data-grid v7->v8. This may mean that a css-loader is required for embedded users due to changes in x-data-grid ([data grid][docs] CSS loader needed for x-data-grid v8.0.0? mui/mui-x#17427)

3.3.0 (2025-04-18)

🚀 Enhancement

• core
  • #4956 Add simplified display of REF/ALT to help with long strings produced by e.g. Cactus VCF (@cmdcolin)
  • #4954 Add genotype frequency table to variant feature details (@cmdcolin)
  • #4952 Add 'genotype' column to the Variant sample grid (@cmdcolin)
  • #4944 Show ALT allele description on multi-variant mouseover (@cmdcolin)
  • #4922 Add Multi-variant SV display (@cmdcolin)
• Other
  • #4950 Add ability to use jexl filters on multi-sample variant displays (@cmdcolin)
  • #4934 Add alpha-transparency to help show overlapping SVs in the Multi-sample variant display (@cmdcolin)
  • #4931 Show target zoom level in tooltip on slider (@cmdcolin)
  • #4930 Upload last release build to https://jbrowse.org/code/jb2/latest (@cmdcolin)
• app-core, core, embedded-core, product-core, sv-core, web-core
  • #4933 Upgrade to MUI v6 -> MUI v7 (@cmdcolin)

🐛 Bug Fix

• Other
  • #4929 Fix broken bigbed features when there is gene level aggregation (@cmdcolin)
• core
  • #4923 Fix dark stock theme showing bad colors (@cmdcolin)

📝 Documentation

• core
  • #4949 Controlling navigation of embedded component - storybook examples (@cmdcolin)
  • #4924 Add config docs for pre-processors with simplified config snapshots (@cmdcolin)
• Other
  • #4925 Update docs with phased VCF tutorial (@cmdcolin)

🏠 Internal

• core
  • #4926 Skip running hydration for server side rendering (@cmdcolin)

Committers: 1

• Colin Diesh (@cmdcolin) Done in 1.41s.
  Done in 0.55s.

---

This discussion was created from the release Release v3.3.0.