IGV 2.11.9 - Dec 2021#

This release includes the following updates:

• The Log4j dependency has been removed from IGV and replaced with java.util.logging. Note, if you have customized Log4j settings in previous versions of IGV, these customized settings are now ignored. Open an issue in the IGV GitHub repo if you need customized log settings.

• Loading of BAM files has been optimized to alleviate bottlenecks affecting large 3rd gen sequencing files and very deep coverage files.

• The function to Move the IGV Directory, which is invoked from View > Preferences > Advanced, now moves the IGV directory to the target directory, rather than moving the contents of the IGV directory to the target directory.

IGV 2.11.7 - Dec 2021#

This release includes the following updates:

• By default, the port listener is disabled on IGV startup. Change the setting in View > Preferences > Advanced. To use web links to IGV or control IGV from other programs, you must enable the port.

• Update to use Log4j version 2.16.0.

• Remove the Color by insert size option for RNA-Seq alignment tracks. This option cannot be meaningfully implemented or interpreted for RNA-Seq data.

• Allow symbolically linked launch scripts. (Git Issue #1060)

• Save the sequence for BLAT tracks in session files. (Git Issue #1065)

IGV 2.11.3 - Nov 2021#

This release includes the following updates:

• The IGV application now starts Java with 8GB max memory by default. The previous default was 4 GB.

• Fixes a problem with loading .gwas files. (Git Issue #1048)

IGV 2.11.2 - Oct 2021#

This release fixes the following issues:

• Selecting File > New Session would delete the reference gene annotation track. (Git Issue #1038)

• For some reference genomes, entering multiple valid gene names in the search box failed to create a multi-locus view and displayed an error message reporting the loci could not be found. (Git Issue #1037)

• Saving images did not take vertical scrolling of tracks into account. For example, when viewing a BAM file, the top alignments in the track were always displayed in the image, even when the alignments in the IGV view had been scrolled to view alignments further down in the pileup. (Git Issue #1033)

• The data range setting on overlaid tracks was not restored when loading a session file. (Git Issue #1026)

• The coverage graph corresponding to an alignment track can now be assigned a color in batch scripts. (Git Issue #993)

IGV 2.11.1 - Sep 2021#

This release includes new batch commands and bug fixes as follows:

New batch commands

The following new commands were added for batch and port execution.

• setColor trackName colorString
• setAltColor trackName colorString
• saveSession filename

See the page describing batch scripts in the User Guide for details on available commands.

Bug fixes

• Fixed a problem that caused the read view of deep coverage alignment tracks to be truncated. (Git Issue #981)
• Fixed a problem that resulted in temporary preference settings from batch and port commands to be save persistently as user preferences.

IGV 2.11.0 - Aug 2021#

This release includes new features and improvements in the following areas:

Loading data from htsget servers

IGV now supports loading BAM, CRAM, and VCF data from htsget servers. Note BCF is not supported. To load data from an htsget server, use File > Load from URL and enter the full URL to the resource. For example,

• https://htsget.ga4gh.org/reads/giab.NA12878.NIST7086.1 (hg38 alignments)
• https://htsget.ga4gh.org/variants/giab.NA12878 (hg38 variants)

Customizing a BLAT service

IGV supports on-the-fly alignment of short sequences by making use of a BLAT web service. For example, from the popup menu in a BAM track you can select to BLAT the read sequence of the selected alignment, or you can BLAT any short sequence by selecting Tools > BLAT in the menu bar. By default, a public service hosted at UCSC is used. This can now be customized in IGV's advanced preferences to use another BLAT service, or a locally executable command line program that returns BLAT-like results. For more details, see the page describing IGV's BLAT search in the User Guide.

User-defined reference genomes

Reference genomes can now be specified and loaded as JSON files, and the previous .genome format is considered deprecated. For more details, see the page on reference genomes in File Formats.

Chromosome ideograms as tracks

UCSC cytoband files can now be loaded as separate tracks via the File menu. (Git Issue #786)

New file format

GenePred Extended files (.genepredext) are now supported. UCSC's gff3toGenePred utility ouputs files in this format.

New batch command

Tracks can now be autoscaled via a batch command: setDataRange auto

Loading data from Amazon S3 time-gated presigned urls

All data formats are now supported when loading from S3 time-gated presigned URLs. (Git Issue #856) See this UMCCR page for details on configuring S3 support.

Bug fixes

• Fixed a problem when displaying "expanded" junction tracks for RNA-seq BAM files. (Git Issue #1018)
• Fixed a problem on Windows when trying to select a new directory for the IGV Directory in View > Preferences > Advanced.