CN

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: http://www.broadinstitute.org/cancer/software/genepattern/gp_guides/file-formats/sections/cn.

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.

Example: mynah.sorted.cn

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.