IGV 2.3, released April 2013

New Features and Improvements

Motif finder. This new feature allows you to search for a particular nucleotide sequence in the reference genome, using either regular expression syntax or IUPAC ambiguity codes. Search results are displayed in two new tracks; one displays matches on the positive strand, and the other displays matches on the negative strand. Read more about it here.

Copy details of alignment coverage track to the clipboard. If you hover the mouse cursor over a sequence alignment coverage track, the pop-up window shows details about the reads at that locus, including the number of reads, and the distribution of called nucleotides. You can now copy this information to your computer's clipboard by right-clicking and selecting Copy Details to Clipboard from the menu.

Improved memory performance for BAM files. In this release, sequence alignments that are no longer in view are purged from memory more frequently than before. "Out of memory" messages should happen less often.

Gitools integration. Gitools is a framework, developed at the Biomedical Research Park in Barcelona (PRBB), for analysis and visualization of genomic data. Data and results are represented as browsable heatmaps. Data can be exported from IGV in gitools format, or loaded directly into a running gitools session. Available under the Tools menu. See http://www.gitools.org for details.

Bug Fixes

Improved parsing of GFF3 files, so alternate coding sequences are displayed properly.
Fixed loading of BAM files over FTP.
Fixed bug where "Load Genome" dialog was sometimes blank.
Set autoscale to false when scale manually set, don't disable "Set Data Range" when autoscale set.
Trim any leading bases from VCF files which match the reference, so variants are displayed where the variation actually starts.

IGV 2.3.2 April 22, 2013

Bug Fixes

Cannot load large tdf or tabix files over http from some servers.

IGV 2.3.3 May 1, 2013

Bug Fixes

Minimum junction setting is ignored in splice junction track.
"Goto mate region" jumps to whole chromosome view when mate is on another chromosome.

IGV 2.3.4 May 13, 2013

Bug Fixes

File handes for "tribble" indexed files are not being closed.
Dragging in split screen / gene list view is broken.
Coverage track height cannot be changed.

IGV 2.3.6 May 2013

Bug Fixes

Null pointer exception creating snapshots from batch script.

IGV 2.3.7 May 30, 2013

The region-of-interest (ROI) batch command now takes an optional "name" argument.

Bug Fixes

When viewing VCF files with large numbers of samples view is not refreshed after scrolling vertically.
IGV fails on startup with Java 8

IGV 2.3.8 May 31, 2013

Bug Fixes

Fails to use proxy settings when performing byte range requests.
Searching for full chromosome causes no view change if already zoomed in

IGV 2.3.10 July 7, 2013

New features and Improvements

Display message when BEDTools plugin encounters an error
Show genomic location in tooltip of alignment tracks
Sashimi plot for RNA-Seq alignments
Option to override user preferences via a batch comman>
Option to direct igvtools output to stdout for count and sort commands, using the special string 'stdout' as the output file.

Bug Fixes

igvtools outputs incorrect wig files (multiple track lines)
SVG files are not readable by some programs (e.g. gimp) on Windows platform due to incorrect encoding.

IGV 2.3.12 July 15, 2013

Bug Fixes

Some bigwig files fail to load with a "null pointer exception"

IGV 2.3.13 August 2, 2013

Pickup default proxy settings from environment variables.

Bug Fixes

UTRs not recognized in GFF files

IGV 2.3.14 August 6, 2013

Implement autoscale for splice junction tracks

Bug Fixes

Loading bedgraph files fail with "array index out of bounds" error

IGV 2.3.15 August 19, 2013

Bug Fixes

Show read sequence of unmapped mates
Exons not associated with transcripts in GTF files
Splice junction tooltip incomplete in collapsed mode

IGV 2.3.16 August 20, 2013

Add "export consensus sequence" option to alignment track menu

IGV 2.3.17 August 26, 2013

Disable native Mac dialog when IGV is launched from Java Web Start

IGV 2.3.18 September 5, 2013

Bug Fixes

Autoscale option is reset after navigating to new locus
Reference sequence track is not shown from session files if there is no assoicated annotation track

IGV 2.3.19 September 27, 2013

Bug Fixes

Popup messages appear when running batch scripts from the command line
Starting from the command line with a session file fails if no genome was previously selected
IGV hangs when viewing soft-clipped alignments at coordinates < 0 (5' end of contig)
Not all exons are displayed from Wormbase GFF files

IGV 2.3.23 October 24, 2013

New Features and Improvements

Add preference to control display of default sample/track attributes
Performance improvements for loading BAM files over the web
Development version only: Remove tracks via delete or backspace key
Allow multiple motifs to be entered at once in MotifFinder
Allow grouping of VCF tracks

Bug Fixes

Starting igv with the -g option causes a null pointer exception when genome is in current directory
Cannot read BAM files when server doesn't return Content-Length
Cannot read eQTL files with missing q-value

IGV 2.3.26 January 17, 2014

New Features and Improvements

Add option to overlay data tracks
A new option for loading files from the ENCODE project has been added to the file menu for genome assemblies hg19, b37, and mm9.
Provide 1-click download of genome and sequence files.
Add additional options for loading files by URL, can specify the index file and TDF file location with "index" and "coverage" query parameters respectively.
Allow EPS snapshot output, through use of EPSGraphics library. See https://www.broadinstitute. org/software/igv/third_party_ tools#epsgraphics for instructions
Add "remove" batch command, syntax "remove <trackName>"
Add 'ctrl-s' hotkey for sorting alignments by most recent sort
Read pairs are now downsampled together (both kept or both removed)

Bug Fixes

Fallback from HEAD to GET for HTTP requests if HEAD fails. Useful for loading from cloud providers such as AWS
When long error messages are displayed, they are scrollable

IGV 2.3.46 March 16, 2015

New Features and Improvements

BLAT. You can now do a BLAT search from a feature, alignment, or region of interest, of up to 8 kb in length as detailed here.
- Features: Right-click on the feature in the track to see the BLAT command in the pop-up menu. The BLAT input sequence is the section of the reference genome defined by the feature start and end bounds.
- Alignments: Right-click on the aligned read to see the BLAT command in the pop-up menu. The BLAT input sequence is the read sequence. It is not the sequence of the reference genome where the read was aligned.
- Regions of Interest: After creating a region of interest, click on the region's red bar to see the BLAT command in the popup menu. The BLAT input sequence is the sequence of the reference genome defined by the region bounds.

By default, the BLAT server hosted at the UCSC Genome Browser is used, but this can be changed in the Advanced preferences (View > Preferences > Advanced). Most UCSC derived genomes are supported, including human and mouse genomes.

Combine numeric tracks. From the Tools menu, you can now dynamically create new tracks by combining two existing numeric tracks. Operators include add, subtract, multiply, and divide. Note that this does not overlay the two tracks, but rather creates a new data track that combines the data values from both tracks. For example, if you multiply two tracks, and one track has a data value of 10 at a particular locus, and the other track has a value of 2 at that locus, then the new track will have a value of 20.

Support for Supplementary Alignments
- Added a new alignment preference to filter supplementary alignments. See Filter and shading options in View > Preferences > Alignments.
- Added Group by supplementary flag to the alignment popup track menu.
- Enhanced the pop-up information panel, also referred to as a tooltip, for supplementary alignments.

Misc
- Session file paths are now relative where possible (i.e. data file path is relative to session path).
- Added a new batch command to go to whole genome view: “goto all”.
- You can now optionally disable quality weighting of the allele fraction when displaying single nucleotide mismatches in the coverage track for sequencing data. See "Filter and shading options" in View > Preferences > Alignments.
- Nucleotide colors for the sequence track are now settable by adding or editing properties COLOR.A, COLOR.C, COLOR.T, COLOR.G, and COLOR.N in the IGV pref.properties file (see the igv directory in your home directory). Similarly for a BAM track with properties SAM.COLOR.A, SAM.COLOR.C, etc., as outlined here.
- The exon numbering scheme has been changed to begin at first coding exon, rather than first exon.
- Increased the keyboard left/right scroll speed to 50 pixels per key press.
- Improved memory management for smaller BAM file footprint.

IGV 2.3.47 March 26, 2015

New Features and Improvements

Add option to filter junctions on Sashimi plot by strand

Bug Fixes

Fix SSL certification errors when running under Java 1.8

IGV 2.3.49 April 10, 2015

Bug Fixes

"Show centerline" ignored if alignment tracks are zoomed out

IGV 2.3.50 April 15, 2015

New Features and Improvements

Option to add gene lists in "bed" format
Add "count as pairs" and "extension factor" options to igvtools input form
Add option to scale fonts for very high resolution displays. If the screen resolution is > 1.5 times the design resolution of 96 dpi all fonts are scaled proportionally. Option is set on the "Genera" tab of the preferences window, default is off (don't scale).

Bug Fixes

Null pointer exception preventing startup when scaling fonts on some machines with very-high resolution screens.

IGV 2.3.51 April 20, 2015

Bug Fixes

Null pointer exception preventing startup when scaling fonts on some machines with very-high resolution screens.

IGV 2.3.52 April 20, 2015

Bug Fixes

BAM files fail to load and hang IGV if server returns a "302" status code for file not found.

IGV 2.3.53 May 26, 2015

Bug Fixes

Bug -- #gffTags ignored if followed by track line
Concatenate bases of leading soft-clip operators

New Features and Improvements

Support for UCSC snp files (extension ".snp").
Check of active port listener before attempting OAuth.
Determine content length of remote file from partial content response header.
Print version update notice to log instead of popup dialog to prevent batch runs from failing.

IGV 2.3.55 May 28, 2015

Bug Fixes

Bug -- ".bam.bai" index file not found in some situations

IGV 2.3.56 June 19 , 2015

New Features and Improvements

Support for proxy "white list"
Improve treatment of cigar operators with padding
Support ".bdg" as a bedgraph file extension
Ignore "YC" tag in bam records if not convertible to a color

IGV 2.3.57 June 19 , 2015

Bug Fixes

Check for "null" gap types when computing splice junctions.

IGV 2.3.58 August 4, 2015

New Features and Improvements

Support for Encode gapped peak files (extension .gappedPeak).
Update htsjdk to version 1.138