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Sample Information

A sample information file (also called an attribute file) is a tab-delimited text file that includes descriptive information (attributes) for tracks. The first column of a sample information file contains track identifiers. Subsequent columns may contain any attribute values and may be given any arbitrary label. For example, the track identifier might be a sample identifier and the attributes might include the patient identifier, gender, tumor/normal, etc. 

IGV matches the track identifiers in a data file with the track identifiers in the sample information file to determine which attributes to display for a track.

Example: exampleSampleInfo.txt

The sample info file plays an important role in integrating diverse data tracks from the same sample or patient.  For example, tracks can be grouped based on the value of an attribute from the sample info file, such as a patient identifier.  Similarly, sample attributes can be used to overlay mutation tracks on other related tracks.

Sample information files can be used to annotate VCF sample rows with metadata, and can be used, for example, to group samples by pedigree or population.

Colors

You can now specify colors for sample information values, either for a specific label or as a heatmap scale for numeric columns.  Colors are specified in a #colors section in the sample information file.  This section is optional; when it is present, it must be the last section.  The general form is tab-delimited, usually with 3 columns (4 columns for a two-color heatmap): 

  • attribute column name
  • attribute value or range
  • color 

An asterisk (*) in either of the first two columns indicates a wildcard.  It is illegal (although not enforced) to have wildcards for both columns.  Some examples follow:

#colors
GENDER    MALE    0,0,155            a value of  "MALE" for the "GENDER" column gets the color (0,0,155)
*    Classical    80,180,80                  a value of "Classical"  in any column gets the color  (80,180,80)
KarnScore    *    0,0,255                   numeric column example, monocolor heatmap
% Tumor Nuclei    90:100    0,0,255       another monocolor heatmap, this time with the range specified.
sil_width    -0.1:0.5    0,0,255    255,0,0             a 2 color heatmap with the range specified.