An LOH file (.loh) is a copy number file that contains "loss of heterozygosity" values. The format is identical to the CN format, but the numbers have the following meanings:

  • -1: Conflict (homozygous in the normal and heterozygous in the tumor)
  • 0: Retained
  • 1: Loss of heterozygosity

Numbers that fall between these values represent the probability of LOH. IGV treats the values as a continuum and colors them according to the heatmap scale set for the LOH track.

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