v3.3.0 Release

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

This PR now allows drawing large structural variants in the multi-sample variant display type. It will actually draw long, even overlapping, structural variants!

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

Loading a random track, and turning on the arc display, there are indications of a large variant for a random sample here (green and navy arcs indicate discordant read pairing associated with inversion)

We hope that you enjoy these new features! The visualizations may be visually complex but we hope it can be a magnifying glass to reveal important patterns of your datasets! Feel free to let us know if you have any feedback

Downloads#

• v3.3.0

To install JBrowse 2 for the web, you can download the link above, or you can use the JBrowse CLI to automatically download the latest version. See the JBrowse web quick start for more details.

3.3.0 (2025-04-18)#

:rocket: 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: 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)

:memo: 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)

:house: Internal#

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

Committers: 1#

• Colin Diesh (@cmdcolin)