Track Line

When IGV loads a data file, it uses the file extension to determine the file format, the file format to determine the data type, and the data type to determine the default display options (see Default Display). Adding a track line to a data file modifies IGV's default display options. This can be particularly useful for file formats not associated with any particular type of data, such as the IGV file format.

The following file formats allow track lines:

  • BED, WIG, PSL
  • IGV, CN, SNP, GFF, LOH, GFF3, SEG -- in these file formats, the track line must begin with a # symbol; i.e. #track

IGV track lines are based on WIG track lines. See the UCSC site for the track line syntax: https://cgwb.nci.nih.gov/goldenPath/help/wiggle.html. The following table describes the track line specifiers that IGV supports. IGV includes a few options that are not part of the UCSC specification.

 

Note: IGV does not currently support multiple track lines in a single file.

Specifier Value Description
name trackLabel Track name (ignored when used in the IGV file format)
description centerlabel Currently ignored
visibility full | dense | hide Currently ignored
color RRR,GGG,BBB Color for positive values in all tracks

altColor

RRR,GGG,BBB Color for negative values in all tracks
priority N Currently ignored
autoScale on|off Currently ignored.  All tracks autoscale unless an explicit data range is defined (e.g., by including the viewlimits specifier).
gridDefault on | off Currently ignored
maxHeightPixels max:default:min default and min are supported
max is currently ignored
graphType bar | points | heatmap

Graph type to use: chart | scatter plot | heatmap.

(IGV only: The heatmap value is an IGV addition to the specification.)

midRange  (IGV extension) x:y

Defines the neutral range for a 3-color heatmap.    Values in this range are rendered with the midColor value,  which is white by default.

Example:  midRange=20:80

midColor  (IGV extension) RRR,GGG,BBB

Color to use in the "mid range" of a heatmap.

Example: midColor=0,0,150

viewLimits lower:upper Defines the data range
yLineMark real-value Currently ignored
yLineOnOff on | off Currently ignored
windowingFunction maximum | minimum | mean | none Function that summarizes the values in a window of data represented by one pixel
smoothingWindow off | [2-16] Currently ignored
url   Defines a URL for an external link associated with this track.  Any '$$' in this string this will be substituted with the item name.
coords  (IGV extension) 0 | 1

Indicate whether the file uses 0 or 1 based coordinates. The UCSC specification for WIG files uses 1 based coordinates and for BED files uses 0 based coordinates. If data looks off by one, check for a possible 0 vs 1 based coordinate issue.

scaleType  (IGV only) log | linear The Y-axis scale type for charts 
featureVisibilityWindow (IGV only)

integer value

The window size in bp below which features are loaded and displayed.  When the viewing window is above this value a message is displayed "Zoom in to view features".  This parameter is useful for  large indexed feature tracks.

A negative value indicate features should be loaded for an entire chromosome (but not the whole genome)

gffTags  (IGV extension) off | on If "on" the name field is treated as a GFF3 style attribute list (column 9 of GFF3).  The default is "off".