IGV 2.12.x

IGV 2.12.0, released January 2022

This release includes the following updates:

New features and improvements:

In this release, we introduce an integration with the IGV-JBrowse Circular View application, which provides a wrapper around the JBrowse circular view component, allowing it to be used directly from within the IGV application. The interactive circular view is useful for exploring structural variants and other long-distance interactions, and can be used with a number of different track types in IGV. See this quick start guide for more details.

Downsampling is now available when viewing interaction tracks (.BEDPE files) in whole genome view.

Session files now support a leading tilda (~) in genome and track file paths. The ~ will be replaced by the path to the user's home folder. (Git Issue #1056)

New batch commands to overlay tracks and separate overlaid tracks. Batch commands are documented here. (Git Issue #118)

Tools > Run Batch Script now supports selecting multiple scripts to run. They will be executed in random order.

Color by > Insert size is now availabe with appropriate defaults for RNA-seq data.

The 3rd Gen preference that enables flag clipping is now on by default, with a threshold of 20 bases.

The options to Hide small indels and Show insertion markers (primarily used for 3rd Gen sequencing data) are now available on a per-track basis from the alignment track popup menu. Previously these were only available through View > Preferences.

Improvements to the test that determines the experiment type (RNA / 3rd Gen / Other) from aligned sequencing data.

Added support for "Squished" mode for variants/sites in VCF tracks (previously only available for the genotypes).

Improvements to better support session files that were created with older versions of IGV.

Bug fixes:

Sometimes a Sashimi plot would display nothing until the view had been zoomed further in. (Git Issue #1087)

View > Fit Data to Window would reset "Type of Graph" for overlaid tracks to the Bar Chart view. (Git Issue #1082)

The red locus indicator on the chromosome ideogram did not update when panning. (Git Issue #1096)

Fixed issue in parsing of track name parameters in batch/port commands - the URL encoding was not being consistently decoded.

Fixed some issues with the layout of the attribute panel that is optionally displayed between the track names and track.

Sometimes the gene annotation track would disappear when FIle > New Session was selected.

This release includes the following fixes:

Sometimes tracks would not load from S3 when IGV was configured for Amazon Cognito. (Git Issue #1101)

VCF tracks were being placed in the Annotation panel by default, rather than the Data panel. (Git Issue #1104)

VCF tracks with only one sample did not show the genotypes section by default. (Git Issue #1104)

Coloring of the allele frequency bars in an alignment coverage track was not taking range thresholding into account. (Git Issue #1100)

If an annotation track was selected, you could not enter a gene name contain 'R' or 'F' in the search box; it was being interpreted as reverse/forward jump command in the feature track.

By default, the port listener is now enabled on IGV startup. Change the setting in View > Preferences > Advanced.