A CN file (.cn) is a tab-delimited text file that contains copy number data. The CN file format is described on the GenePattern web site:

Zero-based index: Physical positions are identified using a zero-based index.

Display settings: To modify IGV's default display settings for the CN data, include a track line in the file.


Does IGV assume log2(ratio) or absolute values for copy number?

IGV looks for the presence of negative numbers.  If it finds them, it assumes that the data is log2(tumor/normal).  If it does not find negative numbers, it assumes that the values are absolute, with 2 as the center.  These assumptions are used to set the heatmap legend; the legend can, however, be changed manually under the View> Color Legends. Instructions are found in the Color Legends section of the user guide.

For data with negative numbers, IGV defaults to a blue-to-red scale that corresponds to copy numbers from -1.5 to 1.5. Both deletions and amplifications can have continuous valued numbers represented by shading.