When IGV loads a data file, it uses the file extension to determine the file format, the file format to determine the data type, and the data type to determine the default display options (see Default Display). In the IGV and segmented (SEG, CBS) file formats, you can use a #type line to override the default data type and thus the default display options. For example, the IGV file format has a default data type of 'Other' and, therefore, the data in file is displayed using a blue bar chart with an autoscaled data range. By adding a #type line to the IGV file, you can indicate that the file contains gene expression data; in which case, the data will be displayed using a blue-to-red heatmap with the data range set from -1.5 to 1.5.
The #type must be the first line in the file. It has the following format:
where data-type is one of the following (these values are case-sensitive): COPY_NUMBER, GENE_EXPRESSION, CHIP, DNA_METHYLATION, ALLELE_SPECIFIC_COPY_NUMBER, LOH, RNAI
The selected data type determines the display settings (see Default Display).