Navigating

Zooming

Zoom out to view the whole genome, zoom in to a chromosome and continue zooming to base pair resolution. As you zoom in, the gene track shows gene names and sequence data. If the sequence data is unavailable, small blocks replace the bases. If you are using a genome stored on the IGV genome server, you must be connected to the internet to view the sequence data.  (Note that the zoom slider, also sometimes called the "railroad track," does not appear when you are viewing the full genome; it reappears when you zoom in to the chromosome level.)

Click the whole genome view icon to zoom out to the genome view.

From the genome view, zoom to a chromosome by clicking its label.

Select a chromosome from the drop-down menu to zoom to it.

Click and drag on the genome ruler to sweep over and select an area to which to zoom.

To zoom in and out on a chromosome:

Zoom in Zoom out
+ -
Double-click or shift-click the track data Alt-click (Mac: option-click) the track data
Click a zoom level on the zoom slider Click a zoom level on the zoom slider
Click the plus (+) icon on the zoom slider Click the minus (-) icon on the zoom slider
Click and drag on the genome ruler to select an
area to which to zoom
 

Scrolling

To scroll the display:

Vertical scroll Horizontal scroll*
Scroll bar in the IGV window Click and drag the track data
Click and drag the track data Click the chromosome ideogram to scroll to that location
Page Up and Page Down keys Click the ruler to center that location
Up and down arrow keys Left and right arrow keys
  Home and End keys (scroll by screen width)

* You cannot scroll horizontally when IGV is displaying the whole genome or a whole chromosome.

Searching

Use the search box to locate:

  • A locus (for example, chr5:90,339,000-90,349,000)
  • A gene symbol or other feature identifier (e.g., DPYD or NM_10000000)
    • When searching features, IGV will accept partial matches. An auto-complete menu will show the possible matches when a partial string is entered; if there are multiple matches IGV will show a dialog asking for clarification
  • A mutation in a feature. IGV accepts 2 mutation formats:
    • Amino acid mutation notation of this form: 
      KRAS:G12C 
      The above would look for a mutation in KRAS on the 12th amino acid, from Glycine to Cystine. 
      * is stop codon
    • Nucleotide mutation of this form:
      KRAS: 123A>T
      The above would look for a mutation in KRAS from adenine to thymine at the 123rd base.
  • A track name (e.g., secondary_GBM_89)
    • IGV searches for an exact match to the name entered in the search box when looking for tracks. For example, entering "secondary" will not locate the "secondary_GBM_89" track.

Note: When loading from a file with an index, search may not find all matches. This is because IGV does not keep the entire file contents in memory when an index is present.

Jumping

If you have a feature track loaded (e.g., Gene track, BED, or GFF file), you can jump from one feature to the next.

  1. Click on the track name to select the track that contains the features that you want to find.
  2. Jump from feature to feature:
    • Press Ctrl+F to jump forward to the next feature.
    • Press Ctrl+B to jump backward to the previous feature.

    IGV positions the start of the next (or previous) feature at the center of the display.

You can also jump from one exon to the next. To exon-jump, select a feature track and press Shift+Ctrl+F to center the next exon in your view, Shift+Ctrl+B to move back one exon.

Back and Forward Buttons

The back and forward buttons in the toolbar () allow you to move backward and forward through your views of the genome the way you move back and forward in a web browser.