A SEG file (segmented data; .seg or .cbs) is a tab-delimited text file that lists loci and associated numeric values. The first row contains column headings and each subsequent row contains a locus and an associated numeric value. IGV ignores the column headings. It reads the first four columns as track name, chromosome, start location, and end location. It reads the last column as the numeric value for that locus (if the value is non-numeric, IGV ignores the row). IGV ignores all other columns.
The segmented data file format is the output of the Circular Binary Segmentation algorithm (Olshen et al., 2004).
Display settings: IGV displays segmented data files using the default track display settings for the copy number data type (see Default Display). To have IGV use the display settings for a different data type, include a type line in the segmented data file.