IGV 2.19.7 - October 2025#

Bug fixes

CRAM files created using LZMA compression could not be read. GitHub issue 1767
There were problems with Sashimi Plots that were opened when the view had been zoomed in to the maximum level, e.g., when a single base had been entered into the search box. GitHub issue 1750

IGV 2.19.6 - September 2025#

New features

Options to support Roche SBX alignments. For details, see the section on SBX alignments options for alignment tracks in the User Guide.
Support for DynSeq rendering of quantitative data files (wig, bigWig, bedGraph, tdf). Right-click on the track and select the DynSeq graph type from the popup menu. The data is rendered as nucleotide-shaped glyphs at high zoom levels and falls back to bar chart rendering at lower zoom levels.

Bug fixes

CRAM version 3.1 is now supported.
For alignment coverage tracks, all read base characters, including ambiguity codes and ‘=’ indicators, are now included in the coverage base counts. Previously non-ATCG characters were counted as “N”. GitHub issue 1707

Bug fixes

Bug fix. Selecting File > Load from Server was not working in the 2.19.3 release.

All WIG, bigWig, and bedGraph tracks are now autoscaled by default.
Attributes in column 9 of GFF files are now searchable by default if they are less than 50 characters long. The old limit was 20 characters. GitHub issue 1681
The filterTypes property is now supported in the definition of GFF and GTF annotation tracks included in reference genomes loaded as JSON files. GitHub issue 1682
Chromosome aliasing for reference genomes hg38 and hg19 has been amended to recognize 23, chrX, and X as the same chromosome.
Bug fix. Setting the view to a multi-locus view in batch scripts was not working.
Bug fix. No tracks were displayed if a session file was loaded that did not have any track panels defined. GitHub issue 1638

New features

Bug fixes

As of version 2.19.1, IGV requires Java 21 or greater.

If you download one of the IGV versions that does not include Java, make sure you have Java 21 installed and in your path.

As of version 2.19.1, IGV Mac apps require MacOS 11 (Big Sur) or greater.

To run the latest IGV on older MacOS versions, download and use the Command line IGV for all platforms option from the main Download page.
To run a working IGV Mac app on older MacOS versions, download the 2.18.4 Mac app (includes Java). Or load any IGV Mac app version 2.18.4 or earlier from the IGV download archive.

New features

New option to download the sequence and/or annotations to local storage when selecting hosted reference genomes. Currently, the default is to use them remotely. For genomes that support downloading, radio buttons will be presented to choose downloading and using the local files instead. The files will be downloaded to the igv/genomes folder, which is usually located in the user home folder.
New options to load ENCODE production release data from the File menu.

Bug fixes