Navigating the view

Navigation controls#

IGV provides several navigation controls for specifying the genomic region to view, which can be the whole genome where all the chromosomes are laid out side by side, a single whole chromosome, or any section of a chromosome all the way down to base-pair resolution. IGV also supports viewing multiple regions side by side, as described in the section below.

To view the whole genome

The screenshot below shows a whole genome view with segmented copy number data. In the area below the tool bar, the tick marks indicate the chromosome boundaries, and each chromosome is labeled.

Whole genome view

To view a whole chromosome:

When viewing all or part of a single chromosome, an ideogram of the chromosome and a ruler indicating the extent of the current region are displayed below the toolbar, and the size of the region and its genomic coordinates are displayed in the toolbar.

Whole chr view

To zoom in and out within a chromosome:

Zoom in Zoom out
Double-click or shift-click on a track; the new view will be centered on the clicked locus Alt-click on a track; the new view will be centered on the clicked locus
Click the plus (+) icon on the zoom slider Click the minus (-) icon on the zoom slider
Click a zoom level on the zoom slider in the toolbar Click a zoom level on the zoom slider in the toolbar
Click and drag on the genome ruler to sweep out an area to which to zoom

When zoomed into a subregion of a chromosome, a red box on the ideogram indicates where the region is located on the chromosome.

Partial chr view

To pan across to neighboring regions within a chromosome:

To jump to another region within a chromosome without changing the zoom level:

To view a specific region anywhere in the genome, use the search box in the IGV toolbar to enter one of the following:

To navigate between features in a feature track (e.g., gene track, BED, or GFF):

To easily navigate between loci of particular interest to you, create a non-indexed BED file of those loci and provide meaningful names to each one. Once you've loaded that file, you can enter the names into the search box or jump to the next/previous locus using the f and b keys.

Viewing multiple regions#

By default, IGV displays one contiguous genomic region, but multiple regions can also be displayed side-by-side in split panels. All the panels in this multi-locus view display the same set of tracks.

Managing the panels#

To enter multi-locus view:

There is no set limit on the number of loci, but if the IGV window is split into too many panels, each one will be too small to be useful.

The following screenshot shows a multi-locus view of segmented copy number data. The IGV data panel has been split into 6 separate vertical panels displaying the regions containing the genes KRAS, MYC, RAC1, RAC2, RAC3, and RAF1.

To rearrange the panels use drag and drop: 

To remove a panel:

To exit multi-locus view:

Controlling the view in a panel#

To zoom the view:

To pan the view:

Sorting tracks by panel#

Right-click in the panel header to bring up the sort menu. This menu will vary depending on data type.

The following image illustrates what happens if you select Sort by amplification in the KRAS panel. All the tracks are sorted by the value in the KRAS panel. Note that each panel displays the same tracks, so the display will change in all the panels.