An IGV file (.igv) is a tab-delimited text file that defines tracks. The first row contains column headings for chromosome, start location, end location, and feature followed by the name of each track defined in the .igv file. Each subsequent row contains a locus and the associated numeric values for each track. IGV interprets the first four columns as chromosome, start location, end location, and feature name regardless of the column headings in the file. IGV uses the column headings for the fifth and subsequent columns as track names. Feature names are not displayed in IGV.

For example:

Chromosome Start End Feature Patient-One Patient-Two Patient-Three
chr1 2150459 2150460 Test_one 0.01 0 0.99
chr1 3558044 3558045 Test_two 0.25 0.71 1.31

Zero-based index: Start and end positions are identified using a zero-based index. The end position is excluded. For example, setting start-end to 1-2 describes exactly one base, the second base in the sequence.

Data must be grouped by chromosome and within each chromosome group sorted by start position: The igvtools package package can be used to sort .igv files.

Display settings: IGV displays IGV file data using default display settings. To modify the default display settings for the  data, you can:

  • Include a type line in the file to make IGV use the display settings for a different data type.
  • Include a track line in the file.