Pop-up Menus

To select tracks and display the pop-up menu, do one of the following:

  • Right-click a track to select it and display the pop-up menu.
  • Right-click an attribute value to select all tracks with that attribute value and display the pop-up menu. Tip: Keep in mind that right-clicking an attribute may select tracks that are not visible in the data panel. Scroll down the data panel to view all the selected tracks.
  • Control-click track names (Mac: Command-click) to select the tracks, then right-click one of the selections to display the pop-up menu.

Commands in the track pop-up menu change the display options for the selected tracks. Most changes made via the pop-up menu are lost when you exit IGV unless you save the session. In a few cases, changing the pop-up menu also changes an option in the Preferences window; these changes are persistent.

The type of data displayed in the selected tracks determines which commands appear in the pop-up menu. This page lists commands by track type: data track, feature track, and alignment track. Use your browser's search function to find a particular command.

Data Track

Data tracks display numeric values. For an example, click File>Load from Server and select The Cancer Genome Atlas.GBM.Expression.GBM Batch 1-8 Centered and Normalized (hg18). The following commands appear in the pop-up menu for data tracks:

Command Description
Track Settings  
Rename Track Renames a track. more...
Change Track Color (Positive/Negative Values) Changes the track color for selected tracks. more...
Change Track Height Changes the track height for selected tracks. more...
Change Font Size Changes the font size for selected tracks.
Type of Graph
Heatmap
Bar Chart
Points
Line Plot
Changes the way IGV displays track data. more...
Windowing Function
10th Percentile
Median
Mean
90th Percentile
Maximum
 
 

Changes the value represented by each pixel of track data.

At all but the lowest zoom levels, each pixel represents a significant amount of data. IGV divides the data to be displayed into "windows" of equal length each corresponding to a single pixel, summarizes the values across each window, and then displays the summarized values in the track. Select the function IGV will use to summarize the values.

Data Range  
Set Data Range Changes the minimum, baseline, and maximum values of the graph used to display track data. more...
Set Heatmap Scale Changes the data range and color of the heatmaps used to display track data. more...
Log scale Plots the chart for that track on a log scale.
Autoscale Toggles the autoscaling function for a given track.  With autoscaling enabled, IGV automatically adjusts the plot Y scale to the data range currently in view.  As the user pans and moves, this scaling continually adjusts.  
Show Data Range Toggles whether the numeric range of the values in the view for a given track is displayed; works for charts other than heatmaps.
Create Overlay Track Merge the selected tracks so that they are displayed on top of one another.
Separate Tracks Only enabled for overlaid tracks. Restores them to separate tracks.
Remove Track(s) Removes selected track(s) from the display. more...
Save image Saves the data visible in the IGV panel to a PNG file.

 

Feature Track

Feature tracks identify genomic features. For an example, see the Gene track, which IGV loads when you select a genome. The following commands appear in the pop-up menu for feature tracks:

Command Description
Rename Track Renames a track. more...
Change Track Color Changes the track color for selected tracks. more...
Change Track Height Changes the track height for selected tracks. more...
Change Font Size Changes the font size of the feature labels.

Collapsed

Expanded

Squished

Displays overlapping features, such as different transcripts of a gene, on one line or multiple lines or condensed (squished).  more...

Copy Details to Clipboard Copies the pop-up text for the selected feature to the system clipboard so that you can paste the information into other applications.
Copy Sequence Copies the sequence of the selected feature to the system clipboard so that you can paste the information into other applications.
Set Feature Visibility Window Specifies the threshold, in kilobases, for IGV to display features in the window. In other words, if you set this at 50 kb, IGV will only display features after you have zoomed in to display 50 kb or less in the IGV window.
Remove Track(s) Removes selected track(s) from the display. more...
Save image Saves the data visible in the IGV panel to a PNG file.

 

Alignment Track

Alignment tracks display alignments (more...). For an example, select the Human hg19 genome from the genome dropdown menu in the toolbar, and then click File>Load from Server and select an alignment from the 1000 Genomes project. Tip: Zoom in to view alignments and the alignment track pop-up menu.

Command Description
Rename track Renames a track.
Copy read details to clipboard When you hover over a read, the tool tip displays information about the read. This option copies that information and the read sequence to the clipboard.
Sort alignments Sorts alignments by start location, strand, base, mapping quality, sample, read group, or insert size (as defined in the BAM file). 
Group alignments Groups alignments by read strand, first-in-pair strand, sample, read group, chromosome of mate, or tag.
Color alignments

Colors alignments by insert size, pair orientation, read strand, read group, or sample.

Regarding the Color by insert size option: 

IGV 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.

Shade base by quality Uses the color intensity of a mismatched base to indicate its quality score: the darker the color the higher the score. Changing this option also changes the option on the Alignments tab of the Preferences window.
Show mismatched bases By default, mismatched bases are displayed as colored letters on a gray bar that represents the read.
Show all bases Select this option to display all bases in the read.
View as pairs For more information on this option, see this page.
Go to mate Jumps to the region of the paired read (if any).
View mate region in split screen

For more information on this option, see this page.

Set insert size options Controls color-coding of paired reads based on the inferred insert size.
Re-pack alignments Sorts alignments to minimize gaps at the top of the track.
Show coverage track When selected, IGV displays the matching coverage track for the alignment track.
Load coverage data

Loads coverage data for an alignment track. To generate coverage data, use igvtools. more...

Loading an alignment track from the IGV data server (File > Load from Server) automatically loads the matching coverage data.

Collapsed

Expanded

Squished

Changes the height of the reads to adjust the amount of information displayed.
Select by name Opens a window so you can enter the name of a read. IGV will highlight that read with a colored border.  Note that IGV does not change the view, so if the read is not currently visible this option will have no apparent effect.
Clear selections

Clears the outlines that show paired reads.

  • Control+click (Mac: Command+click) a read to outline the read and its paired mate in the same color. Colors are arbitrary but unique to each pair. A black outline indicates that the selected read has no mate.
  • To clear the outline for a paired read, Control+click (Command+click) either read.
  • To clear all outlines, right-click and select Clear selectionss
Copy consensus sequence

Calculates the concensus sequence for the region in view and copies the information to the clipboard. The method for calculating the consensus is taken from Cavener, Nucleic Acids Res. 15, 1353-1361, 1987.

1. If the frequency of a single nucleotide at a specific position is greater than 50% and greater than twice the number of the second most frequent nucleotide it is assigned as the consensus nucleotide.

2. If the sum of the frequencies of two nucleotides is greater than 75% (but neither meet the criteria for a single nucleotide assignment) they are assigned as co-consensus nucleotides.

3. If no single nucleotide or pair of nucleotides meets the criteria,  assign an 'N'.

Information copied to the clipboard includes:

  • Locus of the copied sequence (i.e., region currently in view)
  • The consensus sequence.
  • A matrix with the details of all nucleotide counts used to calculate the consensue sequence. Rows in the matrix correspond to the bases along the sequence. The values in a row show the counts for each type of nucleotide at that locus. A header row above the matrix indicates the order of the nucleotide columns (A, C, G, T, and N).
Sashimi Plot Open a Sashimi-style plot window. more...
Remove track Removes selected tracks from the display. more...
Save image Saves the data visible in the IGV panel to an image file