Preferences

To display the Preferences window, click View>Preferences. Preferences are preserved across sessions. To override preferences during a session, use the track display pop-up menu. Each section on this page describes the options on a tab of the Preferences window: General, Tracks, Mutations, Charts, Alignments, Probes, Proxy, Advanced, and IonTorrent.

The last Preference item, IonTorrent is on newer versions of IGV. Screenshots below have been updated only where relevant.

General

Select to distinguish regions with zero values (white) from regions with missing data (gray). Clear (default) to display both regions in the same way (white). Affects only bar charts and scatter plots.
Select to display all tracks in a single panel. Clear (default) to display data tracks (e.g., expression data) in one panel and feature tracks (e.g., genes) in another.
Select (default) to show attributes and attribute values to the left of the data panel. Clear to hide the attributes. This option and View>Show Attribute Display have the same effect on attribute display.
Select to outline the boundaries of regions of interest in black. Clear (default) to leave them without black boundaries.
Zoom in on search results. When selected (default) the zoom level is automatically adjusted so that the target feature fills the view after a successful search. If not checked, the target feature of a search is centered in the view but the zoom level is unaffected.
Change this to change the resolution (in base pairs) at which the sequence track becomes visible.
Change this to define how large a flanking region (in base pairs) IGV will add before and after a feature locus when you zoom to a feature, or when you view gene/loci lists in multiple panels.
Click here to change the background color of the IGV display.
Use this to set a default font size for labeling tracks and features.

Tracks

Default track height for bar charts, scatter plots, and line plots.
Default track height for all other tracks.

Name of an attribute in the sample information file. IGV uses the corresponding attribute value as the track name.

Select to expand feature tracks by default. You may have to restart IGV for this to take effect.

Collapsed:

Expanded:

Select (default) to show the "expand/collapse" triangular icon on feature tracks.

Collapsed with the icon:                          Expanded with the icon:

                           

Select to normalize tracks containing coverage data in .tdf files that were created using igvtools.  This normalization option multiplies each value by [1,000,000 / (totalReadCount)].  This is only available for .tdf files created using igvtools builds dated 1/28/2010 or later.  Earlier versions of igvtools did not record the total read count.

Mutations

Select to overlay mutation data on other tracks. more...
Name of an attribute column in the sample information file. IGV uses the corresponding attribute values to "link" mutation tracks with other tracks. more...
Select this to show mutation tracks that are not linked to other tracks, and therefore will not be seen if the overlay option is checked.  This option has no affect if the overlay option is not selected.

Select to color-code mutation data. Click Choose Colors (or View>Color Legends) to display the Color Legends window, which allows you to view and change mutation color codes.

Charts

Select to add a border at the top to the track.
Select to add a border at the bottom of the track.

Select (default) to color the top and bottom borders (if any). Clear to show the borders in black regardless of the track color. Tip: To change the track color, use the track display pop-up menu.

Select to label the track with its name, provided the track is at least 25 pixels high.
Select to label the y-axis with its data range.
Select (default) to allow charts (barchart, scatterplot, and lineplot) to automatically adjust the plot Y scale to the data range currently in view.  As the user pans and moves, this scaling continually adjusts.  Clear to turn autoscaling off.  There is an option in the popup menu to enable autoscaling for a single track.

Select (default) to show the range of the data.

Select to show all features in heatmaps.

The following figures illustrate these track display options.

  • Color borders selected (default):
  • All options selected:

 

Alignments

Sets the threshold at which IGV displays reads. Reads are visible only when IGV is zoomed in to display a number of bases less than or equal to this threshold.

Downsampling

IGV can randomly sample alignments instead of keeping all of them in memory. The coverage track, displaying total coverage at a region, is unaffected; that is, it always shows unsampled values.

  • Downsample reads: Select to perform downsampling (default).
  • Max read count: The maximum number of reads per window up to 100,000. Default is 100. IGV uses reservoir sampling, so that all reads are kept if the read count is less than Max read count. If the read count is greater, the probability of any given read being sampled is equal to (Max read count) / (actual read count).
  • per window size (bases): Sampling is performed over windows, using the window size specified here.

Filter and Shading Options

  • Coverage allele-freq threshold: Sets the mismatch threshold at which bases on an alignment coverage track are colored.  The default is 0.2, i.e., if a nucleotide differs from the reference sequence in greater than 20% of quality-weighted reads, IGV colors the bar in the coverage bar chart in proportion to the read count of each base (ACGT). The threshold for an individual track can be changed from the pop-up menu.
  • Filter duplicate reads: Clear to display alignments marked as duplicate reads.
  • Filter vendor failed reads: Select (default) to filter out reads that fail the vendor quality check.
  • Flag unmapped pairs: Select to draw a red box around any paired alignment whose mate is not mapped.
  • Show center line: Select so that, when zoomed in sufficiently, IGV displays a line at the center of the display. At higher resolutions, the center line becomes two lines that frame the aligned bases at the center of the display, as shown in the figure above.
  • Filter alignments by read group: Select to hide alignments that match the read groups listed in the filter file. The filter file is a text file that lists read groups, one per line.  This option means that IGV does not load the alignments associated with these read groups. Specify a URL or absolute file path to the file.
  • Mapping quality threshold: Sets a threshold on alignment mapping quality. Only alignments with mapping quality greater than or equal to this threshold are shown.
  • Show coverage track: Select to display a coverage track for each alignment track. The coverage track is visible only when alignments are visible. It displays a gray bar chart showing the depth of the reads at each locus. If a nucleotide differs from the reference sequence in greater than 20% of quality-weighted reads, IGV colors the bar in proportion to the read count of each base (A, C, G, T). Modifying this option affects the display of subsequently loaded alignment tracks. Note, to change the threshold from the default 20%, see Coverage allele-freq threshold.
  • Show soft-clipped bases: Select to show the soft clipped sections of the read.
  • Flag zero-quality alignments: reads mapping with quality scores of zero are flagged in white. Changing this preference requires reloading of data to take effect.
  • Shade mismatched bases by quality: Select (default) to shade mismatched bases by quality.  The letters representing bases of lower quality will be more transparent, while higher-quality bases will appear more solid.

Splice Junction Track Options

  • Show junction track: Select to display the splice junction track.
  • Min flanking width: The minimum amount of nucleotide coverage required on both sides of a junction for a read to be associated with the junction. This affects the coverage of displayed junctions, and the display of junctions covered only by reads with small flanking regions.
  • Min junction coverage:  The minimum number of reads associated with a junction required for the junction to be displayed.
Sets default size thresholds for color-coded flagging of paired end alignments. Only paired end alignments with insert sizes between these thresholds are flagged.  Select Compute to compute selected values from the actual size distribution of each library.

 

 

Probes

Select an option to determine how IGV places expression data on the genome:

  • Map probes to target loci: Use the probe ID to determine the probe locus and display data at that location. If that fails, map the probe ID to a gene, determine the gene locus, and display data at that location.
  • Map probes to genes: Map the probe ID to a gene, determine the gene locus, and display data at that location.

Modifying this option affects the display of subsequently loaded alignment tracks.

Proxy

Sets proxy parameters for connecting to the Internet.  IGV will use this to load hosted genomes and hosted data sets.
Select and enter values if a username and password is required for the proxy.
Clears all proxy settings.

Advanced

Select this option to enable a port on which IGV listens for commands and http requests. Enabling the port allows control of IGV from a web browser. more...

Select this option to edit URLs for the IGV data and genome servers. These settings are rarely changed. 

IGV caches each genome that it loads. On rare occasions, it may be necessary to clear the cached genome file to display an updated version of the genome. Click Clear Genome Cache to do this.

Genome Server URL is the URL for the genome server that populates the genome drop-down list.

Data Registry URL is the URL for the hosted data sets registry (populates File>Load from Server dialog).

Keep this selected to allow IGV to automatically check for updated genomes. Clear to disable this automatic check.

IGV 2.2, released December 18, 2012, and newer versions allow disabling anti-aliasing. This can significantly improve performance in some circumstances with running with X-Windows.

This allows you to move your default IGV directory.

 

IonTorrent

Flow signal distribution chart options
Server settings