Segmented Data

File Format

For segmented copy number data, use the SEG or CBS file format.

Display Notes

• By default, IGV displays segmented data as a blue-to-red heatmap where the data range is -1.5 to 1.5. If loaded segmented data appears in tracks colored all red, check the data values and modify the data range as necessary.
• To change track display options, use the track pop-up menu. The commands that appear in the pop-up menu are those relevant to any data track.

Gaps Between Segments

By default, IGV fills the gaps between adjacent segments by extending the segment endpoints. When zoomed in sufficiently, error bars indicate the gaps:

Alternatively, you can leave the gaps between the segments. In this case, the gaps appear gray:

To modify how gaps are displayed  between adjacent segments set the "Join Adjacent CopyNumber Segments" option on the General tab of the Preferences window.