IGV 2.11.9 - Dec 2021#

This release includes the following updates:

IGV 2.11.7 - Dec 2021#

This release includes the following updates:

IGV 2.11.3 - Nov 2021#

This release includes the following updates:

IGV 2.11.2 - Oct 2021#

This release fixes the following issues:

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.

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

Bug fixes

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,

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