IGV 2.11.x

IGV 2.11.0, released August 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,

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 https://github.com/igvteam/igv/wiki/Customizing-BLAT.

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  https://github.com/igvteam/igv/wiki/JSON-Genomes.

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 <track name>

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.

IGV 2.11.1, released September 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. See the commands wiki page for more details

  • setColor trackName colorString
  • setAltColor trackName colorString
  • saveSession filename

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.