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IGV 1.1 New in this releaseIGV 1.1, released September 2008, includes the following new features and improvements:. Load from server.

Select FileLoad from server to load genomic data from a public server hosted by the Broad Institute. As of September 2008, the public server holds datasets from the Cancer Genome Atlas (TCGA) project (see ).

Fit to window. Select TracksFit to Window to modify the track height so that all tracks are displayed.

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For very large datasets, IGV sets the track height to the minimum value of 1 pixel. Set track height. The menu items TracksSet Default Track Height and TracksReset Tracks have been replaced with a single menu item: TracksSet Track Height. To set the default track height, use the Preferences window (ViewPreferences). Mutations. Hovering over a mutation 'overlay' now displays the mutated base rather than the underlying track name.Fixed in this releaseIGV 1.1 corrects the following known issues:.

IGV now ensures that track height is saved as an integer. Previously, saving track height as a non-integer occasionally prevented IGV from starting. Restoring a session no longer requires a refresh.

Previously, when you restored a session, the search box displayed the saved genome location but you occassionally had to click the Refresh icon to correctly display that portion of the genome. The IGV User Guide now correctly documents the delimiters in the GCT file format: In the second column of the GCT file, the Description column, include the HUGO gene symbol or chromosome location within the delimiters @ and. IGV 1.2 New in this releaseIGV 1.2, released December 2008, includes the following new features and improvements:. Additional genomes.

Genomes are continually being added to the IGV genome server. As of this release, IGV supports the following genomes: Human (hg18, hg17, hg16), Mouse (mm9, mm8, mm7, mm6, mm5), Chicken (galGal3), Plasmodium (3D7 v2.1), Yeast (S. Cerevisiae, S.

Pombe), Zebrafish, Neurospora crassa (v3), and T. Castaneum (2.0). For a current list of supported genomes, click the genomes drop-down list in the IGV tool bar.

Import genomes. Genomes that are not yet available on the IGV genome server, can now be imported into IGV.

To import your favorite genome, click FileImport Genome. See for details.

Support for probe identifiers. When loading a GCT or RES file, IGV now recognizes Affymetrix, Agilent and Illumina probe identifiers and automatically places the gene expression data at the correct loci.

See for details. Search feature tracks. The search box in the IGV tool bar now allows you to search for a locus (for example, chr5:90,339,000-90,349,000), gene (for example, DPYD), or any feature in a feature track (for example, NM10000000). New display options. IGV displays track data using a heatmap, bar chart, or scatter plot. IGV now provides several additional display options for bar charts and scatter plots. See the window for details.

General Feature Format (GFF) file support. IGV can now load genomic features from GFF2 or GFF3 files. For IGV, use the.gff file extension for GFF2 and the.gff3 file extension for GFF3 files. See the Wellcome Trust Sanger Institute web site for a description of the GFF2 file format. See the Sequence Ontology Project (SO) web site for a description of the GFF3 file format. Wiggle (WIG) file support. IGV can now load a feature or data track from a wiggle (WIG) file.

The file must have a.wig file extension. See the USCS Genome Bioinformatics web site for a description of the wiggle (WIG) file format. IGV 1.3 New in this releaseIGV 1.3, released May 2009, includes the following new features and improvements:. View sequence alignments. Sequence alignments in SAM and BAM file formats ( can now be viewed in IGV. See for details. Use FileLoad from Server to view sample datasets from the 1000 Genomes project.

Note that BAM files must be indexed, and SAM files must be orderd by alignment start location. It is reccommended that large SAM files be converted to BAM format prior to viewing. IGV also provides limited support for alignments in the sorted.txt output from the Illumina Pipeline Version 1.3. See for details.

Enhanced RNAi support. IGV now includes enhanced support for loading and viewing RNAi datasets based from the RNAi Consortium shRNA library (See for details. Enhanced gene expression support. IGV now includes the option to map expression data to the chromosome using probe locations (when available) rather than genes. See for details. New display features. With this release, IGV adds a number of new features including the ability to rename tracks, rearrange tracks via drag-and-drop, search for tracks by name, and display track data using line plots.

Performance improvements. IGV loads and displays all ASCII file formats (bed, wig, gct, igv, cn) significantly faster. Additional genomes.

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The following genomes have been added to the IGV genome server since the December 2008 release of IGV 1.2: Human assembly b36 (the reference genome for the 1000 Genomes project), Plasmodium falciparum assembly 3D7 v5.5, C. Elegans assemblies ce6 and ce4, D. Melanogaster assemblies dm3 and dm2, and O. Sativa release 6. For a current list of supported genomes, click the genomes drop-down list in the IGV tool bar. IGV 1.3.1 New in this releaseIGV 1.3.1, released June 2009, includes the following new features and improvements:. Clipped alignments.

Clipped alignments annotated with 'S' in SAM CIGAR strings are now displayed properly. IGV now displays only the aligned portion of a read, ignoring the clipped bases. Saving read details. A new menu item has been added to the alignment popup menu to copy the read details to the clipboard.

This includes the popup text and the read bases. Image output. The image export feature has been reimplemented to fix several critical bugs. The new version includes an improved implementation for enacapulsated postcript output. Support for svg and pdf output has been removed. Linux peformance bug. A bug involving keyboard managment that would cause IGV to freeze on some Linux releases has been fixed.

Performance improvements. Performance has been improved significantly for viewing alignment tracks with very deep coverage, and for loading large copy number files. IGV 1.5.xI GV 1.5.64 released April 2011.Change to 'whole genome' view.

Released June 30, 2010New File Menu OptionsDistributed Annotation Server (DAS) support. There is now an option under the File menu to load features from a DAS server. This option is experimental and subject to the following limitations:.The segment parameter is ignored; features will be loaded per chromosome on demand.No validation is done of the DAS source with respect to the currently selected genome.An example DAS URL, valid for hg18 and b36, is:.Batch Execution. There is now an option under the File menu for users who want to execute a series of sequential tasks: FileRun Batch Script. Users can load a.txt file that contains a list of commands, one per line, that will be run by IGV.

The accepted commands are the same as the IGV Port Commands as seen here:.New Preferences OptionsChange to Treatment of Segmented Copy Number files. Space between adjacent copy number segments now appears gray by default. To enable the joining of adjacent copy number segments, select ViewPreferencesGeneral tab and select the checkbox for Join Adjacent CopyNumber Segments.Coverage (.tdf) Track Normalization. There is a new option to normalized coverage tracks computed with igv tools.

This normalization option multiplies each value by 1,000,000 / (totalReadCount). Enable this option by selecting ViewPreferencesTracks tab and selecting the Normalize Coverage Data checkbox.This is only available for.tdf files created using igvtools builds dated 1/28/2010 or later.

Previous versions of igvtools did not record the total read count.Dynamic Autoscale. By default, charts (barchart, scatterplot, and lineplot) now automatically adjust the plot Y scale to the data range currently in view. As the user pans and moves, this scaling will continually adjust. To turn autoscaling off by default select ViewPreferences Charts tab and uncheck the option. This option can also be set for a single track from the popup menu.Allele Frequency Threshold.

Users can now set the mismatch threshold at which bases on an alignment coverage track are colored. To change the default threshold, select ViewPreferences Alignments tab. The default of 0.2 can be changed in the Coverage allele-freq threshold field. The threshold for an individual track can be changed from the popup menu.Proxy Settings. Proxy settings are now supported for accessing the IGV genome and data server from behind a firewall. Specify the proxy setting by selecting ViewPreferencesProxy tab.Other ImprovementsPostscript output replaced by SVG.

The postscript (.eps) output option has been replaced with scalable vector graphics (.svg).Improvements to Sessions. Many bugs related to restoring sessions have been fixed. The changes should be backward compatible with 1.4.2 sessions.Genome Import. When genomes are imported from a single FASTA file, the order of the sequences within the FASTA are maintained in the Chromosome drop-down list.Password-protected Files.

Basic authentication is now supported for files loaded by HTTP. For information on how to set up an Apache server directory to be password protected, see.BED File Support. The UCSC track line options itemRGB, useScore, and url are now supported.Heatmaps. Heatmap scale settings can be set per track.New File Formats.MAF files are supported for mutations. The file extension must be '.maf'.Birdseed files are supported for copy number. The file extension must be '.birdseyecanarycalls'.Arguments for Command Line Startup.

Users who start IGV from the command line can now specify a single session file or a comma-delimited list of files (as the first argument in the command), and can add a locus string or gene to zoom to as a second, optional argument.Exporting Selected Nucleotide Sequences. Users can now copy the sequence of a feature or region to the clipboard. To copy the sequence of a feature, right-click on the feature and select Copy Sequence. To copy the sequence of a region:.Click the Define a region of interest icon in the tool bar.Click the red bar above the data panel and below the chromosome map that represents the region.Select Copy Sequence in the popup menu.Indexed BED and VCF files. Large BED and VCF version 3.2 files can now be indexed with IGVTools (1.5). IGV 2.0 Feature GuideIGV 2.0This guide details major feature updates for IGV version 2.0.

New Java RequirementIf you are launching the IGV client and you encounter an error message that tells you that you have a bad version number, ensure that you are running Java 6.IGV 2.0 requires that Java 6 or later be installed on your computer (previous versions of IGV required Java 5 or later). If you do not know which version of Java you are currently running, try running this Web site:.For Windows: Java version 6 is available for download from Sun.For Macintosh: All Macs running Leopard or after should have Java 6 installed on them. On some Macs the download fails when launched from Firefox 3.x. The error message under 'details' will say something about an unsupported class version.

For unknown reasons, Firefox sometimes tries to launch the app with Java 5, rather than Java 6. Safari launches correctly, as does Firefox 4.x. If you get this error, Java 5 may be the current default. In order to set Java 6 as the default on Leopard:.Open ApplicationsUtilitiesJavaJ2SE 5.0Java Preferences.In the Java Application Runtime Settings section, drag J2SE 6.0 above the other J2SE items.In order to set 6 as the default on Snow Leopard:.Open ApplicationsUtilitiesJava Preferences.In the General tab, make sure the Java SE 6 checkbox is the only one selected and drag that line to the top of the list.If you don't have 6 on your machine, Apple supplies their own version of Java. Use the Software Update feature (available in the Apple menu) to check that you have the most up-to-date version of Java for your Mac.If you are unable to resolve this issue, please post a help request at the.IGV 2.0 FeaturesIGV 2.0 includes:.New NGS functionality: split screen view, view as pairs, splice junctions, Goby support, and new pop-up menu options.New options for.New options for.The ability to use.New and options.The new, to help track and navigate to your Regions of Interest.The ability to and color scales for sample attributes.Other new functions are listed below. New Sequence Track Pop-up Menu Options Sort AlignmentsThere is a new option to sort alignments by insert size. Set Maximum Coverage Depth.IGV now allows you to Set maximum coverage depth.

IGV downsamples reads if the depth exceeds that threshold. Color AlignmentsThere are now options to color alignments:. by insert size. by read group. by sampleDetails About the by insert size OptionIGV uses color coding to flag anomalous insert sizes.Blue is for inserts that are smaller than expected. That is, the inferred insert size on the reference genome is smaller than expected given the actual insert size.Red is for inserts that are larger than expected. That is, the inferred insert size on the reference genome is larger than expected given the actual insert size.

View As PairsFor more information on this option, see. View Mate Region in Split ScreenFor more information on this option, see. Track SettingsThere are now three ways to view the tracks: Collapsed, Squished, or Expanded. New NGS FunctionalityNew NGS functionality includes:.a, invoked by right-clicking over an alignment and selecting View mate region in split screen from the drop-down list.a, where paired-end reads are drawn as a single 'template', with a connecting line joining the two pairs; invoke by right-clicking over the alignments and select View as pairs.the ability to as an alternative representation of.bed files encoding splice junctions, such as the 'junctions.bed' file produced by the program.

IGV 2.2.x IGV 2.2 released December 18, 2012. Improved interface for loading and managing genomes. In previous releases, the genome drop-down menu listed all genomes that are available in IGV. However, the list of hosted genomes has grown beyond the point where it is manageable in a single dropdown. In IGV 2.2 you can customize the drop-down menu to include only the genomes that are of interest to you. The genome menu now initially lists only a small number of default genomes, but you can add genomes to the list, remove genomes from the list, and rearrange the order of genomes in the list.

See. Integration with BEDTools. Is a fast, flexible suite of tools that can be used to compare sets of genomic features. IGV can now use BEDTools to compare features in loaded tracks, and view the results as a new track. Note: This is currently not supported on Windows. Integration with GenomeSpace.

Is a system that bridges the gaps between bioinformatics tools, making it possible to move data smoothly between tools, leveraging the available analyses and visualizations in each of these tools. IGV is one of the founding tools in the GenomeSpace initiative. See. New menu bar layout. The main IGV menu bar layout has been updated to accommodate the new features described above. There are now three new items in the menu bar:.

Genomes. Items related to loading and managing genomes have been moved out of the File menu, and into their own menu. Tools. Items related to external tools have been moved out of the File menu, and into their own menu. Use the Tools menu to run the BEDTools functions, igvtools, and IGV batch scripts. GenomeSpace. Items related to GenomeSpace are in their own menu. Network view. IGV can now connect to the to display information about networks of genes. An IGV gene list is used to provide seed genes to the cBio portal, which then displays a network of the seed genes and their neighboring genes. You can filter the network based on mutation, copy number, and expression data that you have loaded into IGV.

See. Alternate coding sequence translations. When the view is zoomed in to display individual nucleotide bases in the sequence track, IGV displays the 3-frame translation to the corresponding amino acid sequence. You can now select from 18 alternate.

Enable this view and select the translation table by right-clicking on the sequence track. New option for pop-up details.

By default, when you hover over an element in the data panel you will see a pop-up display with details about the element. You can now choose to only display the details when you click on the element. You can also disable the pop-up so that it is not displayed at all. Click on the yellow balloon icon in the IGV tool bar to specify the behavior you want.

New options for grouping sequence alignments. Two new options have been added to the menu for grouping alignments: for paired alignments, you can now group by mate chromosome or pair orientation. New file formats. IGV now supports (.gbk) files, and the ENCODE and formats. IGV 2.3.xIGV 2.3, released April 2013New 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. 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. IGV 2.4.xJava 8 is now required. IGV 2.4 requires Java version 8 to run. The latest version of Java can be downloaded from. Note that older versions of IGV are always available via the Archived Versions link on the IGV Downloads page. IGV 2.4.0, released September 20171. Support for PacBio long-read sequencing data. PacBio reads are long (up to 50kb) and have a high rate of small random errors that can clutter the view.

However, because the errors are random, quality is extremely high in a consensus of independent reads and a mismatch that is consistent across reads indicate biological variation. IGV 2.5.x IGV 2.5.0, released March 2019IGV has been updated to work with Java 11 and the (free) OpenJDK version of Java.There are no new features in IGV 2.5.0, but significant changes to the IGV code base were required to work with the new version of Java. IGV 2.5.1, released April 2019.Fixed bug: Clicking on the red Region of Interest bar did not bring up the menu.IGV 2.5.2, released April 2019.Fixed issue with loading indexed files from AWS signed URLs.IGV 2.5.3, released May 2019.Modified Windows NSIS installer to allow private installs.Fixed bug: Proxy passwords were stored in plain text.

IGV 2.6.xIGV 2.6.0, released July 2019This release includes a number of new features and fixes:.files are now supported. They are drawn as arcs, either as nested arcs or proportional to score.GATK's MAFLITE mutation file format is now supported.Popover text windows for mutations now include links to more information in CRAVAT at.

Enabled when viewing data with reference genome hg38.Files in Dropbox can now be loaded into IGV. Use the File Load from URL menu.The level of transparency can now be adjusted in tracks that combine multiple overlaid tracks. Use the option provided in the track's popup menu.Tracks in the current IGV session can now be re-loaded using File Reload Session. All the data tracks will be re-loaded, but the view and other settings remain the same.The CTRL-F and CTRL-B feature for jumping to the next/previous variant site in a VCF track can now skip sites that are filtered out.

If you select 'Hide filtered sites' in the track's popup menu, any filtered sites will not be displayed and will not be included when jumping between sites. A checkmark will appear next to the menu item to let you know that those sites are not displayed in the track. Note that in previous versions of IGV, this menu item was named 'Suppress filtered sites' and there was a bug that prevented jumping to the next/previous site if it was checked.Popover text when hovering over alignments in BAM tracks can now display CIGAR string lengths of up to 1000 (was 60).IGV 2.6.1, released July 2019.Fixed bug where altColor specified in #track line was ignored by feature tracks.Updates to new arcs support introduced in 2.6.0.Accept '.' As valid score in BEDPE files.Support HICCUPS files.IGV 2.6.2, released August 2019.Fixed problem reading non-indexed annotation files by URL.IGV 2.6.3, released August 2019.Fixed bug where a local FASTA file for a custome genome was also deleted from the file system when the genome was removed from the IGV dropmenu via Genomes Remove Genomes.Fixed a problem that affected reading some gzipped files and produced the error message 'Unable to create BasicFeatureReader using feature file, for input source '. IGV 2.7.xIGV 2.7.0, released October 2019This release includes a number of new features and fixes:.Support for viewing data in Amazon S3 storage using native AWS authorization and authentication. Contributed by Roman Valls Guimera , Florian Reisinger, and Oliver Hofmann from the University of Melbourne Center for Cancer Research (UMCCR), and Andrew Patterson from the Melbourne Genomics Health Alliance. See the for details on using this feature.Mutations in MUT and MAF files are now colored by mutation type by default.

This can be disabled in the View Preferences Mutations tab. The mutation colors can also be changed in the Mutations tab; note they are no longer in the View Color Legends window.Viewing data via public Google URLs no longer requires a Google login.The 'useProxy' option is now ignored unless proxyHost is set. In previous versions of IGV, a null proxyHost would cause the application not to launch if 'useProxy' was set.Fixed an issue where index files were not always correctly recognized. For example, the file bamfile.bai was not always automatically loaded as the index file for bamfile.bam.Updated line plots.Fixed several issues related to sessions:.Sessions were not correctly handling relative file paths. This was fixed, and sessions now use relative paths by default.Group autoscale now works for overlaid tracks loaded from a session.The state of 'showDataRange' is now saved in session files.

Regions of interest were not displayed when imported from a BED file with chromosome names without the 'chr' prefix. IGV 2.8.xIGV 2.8.0, released January 2020This release includes the following new features and improvements:1. Sequence alignment tracks.A number of default values are set based on the sequencing experiment type, which is inferred from the alignments when they are first loaded from the file, i.e., when the view is sufficiently zoomed in to a region that contains alignments. The alignment track popup menu now includes a new item where the experiment type can also be set explicitly. Values include: 'RNA', '3rd Gen', and 'Other' (the default). Note that any values that are set based on experiment type can be overriden in the preferences ( View Preferences).The Copy read sequence command in the track popup menu is now available when viewing alignments as pairs.BLAT searches can now be performed on soft-clipped sequences (if at least 20 bp in length).Sorting alignments by start position now uses the first mapped base and ignores any soft-clipped bases.Fixed an issue with the read details presented in the popup text for read string = '.' .

The length was incorrectly presented as 1bp; it is now reported as 'undefined'.The Alignments tab of the Preferences window has a new option to specify the default display mode for alignment tracks. It can be set to EXPANDED, SQUISHED, or COLLAPSED. The display mode for an individual track can be changed via its popup menu.The option to filter alignments by read group is back in the Alignments tab of the Preferences window.

It had inadvertently been dropped in a previous release.2. Translation view in reference sequence track.Coloring of start codons was previously based on the amino acid, not the codon. This meant that Methionine (M) was colored green whereever it was found, which is not always correct (e.g. For the Mitochondrial table). Now AUG/ATG are colored green. In addition, the genetic code tables can now include alternative start codons that are colored yellow. Specifically, for Vertebrate Mitochondria these are AUA, AUU, and AUC.In previous releases, the amino acids in view were not always updated when a different translational table was selected.

This has now been fixed.3. Sample attributes.New feature: Overlay tracks based on a shared sample attribute via Tracks Overlay.New feature: Rename tracks based on a sample attribute via Tracks Rename.Renaming a track via the popup menu no longer disables its sample attributes. The attribute key is now the original track name, and so the track retains its sample attribute assignments when it is renamed.Coverage and splice junction tracks for a.bam file are now assigned the same sample attribute information as the associated alignment track.Reinstated the option to specify a sample attribute key to use for track names by default. This option was inadvertently dropped from the Tracks tab of the Preferences window in a previous release.Fix to allow the #sampleMapping section to stand alone in a separate text file. The behavior now matches the description in the user guide.4.

Other new features and improvements.Resize an existing Region of Interest by CTRL-clicking on its red region bar below the genome ruler and dragging to the new start or end position.Change the view locus by dragging the red box in the cytoband view.Add a new empty data panel to the display via View Add New Panel. Move tracks into the panel by selecting the track names and dragging them to the new panel.dbSnp searches are now supported for the following assemblies. Enter the SNP's RSID, e.g. Rs172334, into the locus search box.Human hg19 and hg38; dbSNP build 151 (source UCSC Browser). Common SNPs, i.e.

Found in = 1% samples. Flagged SNPs, i.e. Rare, but flagged as clinically associative by dbSNP.Mouse mm10; dbSNP build 142 (source UCSC Browser). Common SNPs, i.e.

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Found in = 1% samples.New file type: Files of type regionPeak are now supported and are treated the same as.New options when running IGV from the command line.help will print a list of available command-line options and then exit.version will print the IGV version and then exit.Fixed an issue with the display of read coverage in Sashimi plots. Sometimes the coverage seemed to disappear in zoomed out views. The menu that connected IGV to GenomeSpace has been removed. With the discontinuation of NHGRI funding for the GenomeSpace project its servers have now been shut down.

See for more details. IGV 2.8.2, released March 2020New features and bug fixes since the IGV 2.8.0 release include ( note, there was no 2.8.1 release):.New option to sort sequence alignments by 'read name' in the right-click popup menu.When loading a new sequence alignment track, the default is now to shade bases by quality. This preference can be changed in View Preferences Alignments. The min and max value thresholds for the shading can also be set in the preferences.When showing soft-clipped bases is enabled, you can scroll beyond the beginning/end of the reference sequence. Previously the max extension was hardcoded at 1000 bp; the exentension window size can now be set in View Preferences Alignments.Bug fix: Saved session files did not store the state of hidden junction tracks or the new name of renamed coverage tracks. This has now been fixed.Entering.

in the locus search box will now display the whole-genome view. Other ways to accomplish the same thing include: entering All into the search box; selecting All from the chromosome dropdown menu; clicking on the 'whole genome view' icon in the toolbar.

File Reload Session now reloads the most recently opened or saved session file.Currently loaded tracks can now be reloaded from file by selecting File Reload Tracks or by clicking on the 'refresh' icon in the toolbar.Bug fix: GWAS track names are now displayed correctly.Fix for Catalina MacOS: The igvtools file dialog has been updated to work with the restricted folders on Macs running Catalina.

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