Sample Information
A sample information file (also called an attribute file) is a tab-delimited text file that includes descriptive information (attributes) for track identifiers. For example, the track identifier might be the sample identifier and the attributes might include the patient identifier, gender, tumor/normal, etc. The first column of a sample information file is usually labeled Array and contains unique track identifiers. Subsequent columns may contain any attribute values and may be given any arbitrary label.
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: example_sampleinfo_LINKING_ID.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 base don the value of an attribute from the sample info file, such as a patient identifier. Similarly, sample attributes are used to overlay mutation tracks on other related tracks.
Display Attributes in a Sample Information File
Sample attributes can also be used to specify how tracks should be displayed in IGV. By default, 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). Adding display attributes to the sample information file overrides the default display. For example:
| Array | Track_ID | Type | #COLOR | #height | #graphType |
|---|---|---|---|---|---|
| AA_1 | 102 GP needle_20050817 | glioma | 0,0,0 | 50 | bar_chart |
| AA_2 | 102 GP needle_20050817 | glioma | 0,0,0 | 50 | bar_chart |
The following table lists the valid display attributes. Each attribute label must be preceded by a # or IGV will not change the display to match the specified values. The attribute labels are case-insensitive; for example, #color, #Color, and #COLOR are equivalent.
| Attribute Label | Definition | Permitted Values |
|---|---|---|
| #height | Track height, in pixels | An integer > 0 |
| #max | Maximum data value | An integer that is > #min value |
| #min | Minimum data value | An integer that is < #max value |
| #mid | Data value baseline | An integer whose value is between the value set for #max and #min Usually this value is set to 0. Sometimes copy number data is set to 2. |
| #graphtype | Graph type used when the data initially display | One of the following:
#graphtype=scatter_plot |
| #color | Color used for positive values in bar charts and scatter plots | A comma-separated three-value RGB specifier of the form [RRR, GGG, BBB], where each value may be a number from 0 to 255. Example: #color=0,0,0 |
| #altcolor | Color used for negative values in bar charts and scatter plots | Same as for #color |