Mutation Files

File Formats

Mutation data is loaded from a .mut file.   The resulting values can be visualized as distinct tracks or overlaid on other associated tracks (e.g., expression or SNP data from the same patient).  This association is specified by means of a special "linking" column in a sample information file.   By default IGV looks for a column with the heading LINKING_ID for this association, but the exact heading is configurable as a user preference under the Mutations tab of the Preferences window.   Mutations are overlaid on another track when the values of this column are equal.   A typical use case is to record an identifier identifying a patient, or sample, in this column.

To visualize mutation data:

  1. Format mutation data using the MUT file format; e.g., example.mut.
  2. Format the data from platform-specific assays using an appropriate file format; e.g., example.gct (expression data) and example.seg (segmented copy number data).
  3. Define attributes and their values in a sample information file; e.g., example_sampleinfo_LINKING_ID.txt. A sample information file contains a row for each track and a column for each attribute:
    The first column contains track identifiers. The track identifier for each mutation track and each associated data track must be included in the sample information file. The track identifiers can be found in the data files (e.g., example.mut, example.gct, and example.seg).
    Each subsequent column identifies an attribute and its value (if any) for each track. IGV uses the value of one attribute (by default, LINKING_ID) to link mutations to associated data tracks; a mutation track and data track that have the same value for this attribute are linked.

 

 

In the example sample information file, the LINKING_ID attribute (2nd column) links the mutation and data tracks. However, in practice, it might be easier to use an existing an attribute rather than adding a LINKING_ID attribute. Notice that, in this example, the LINKING_ID and Sample attributes have the same value. The LINKING_ID attribute could be removed from the sample information file and the Sample attribute used to link the mutation and data tracks. By default, IGV uses the LINKING_ID to overlay mutations on data tracks. If you use an attribute other than LINKING_ID, enter that attribute name on the Mutations tab of the Preferences window

Display Notes

By default, IGV displays mutations (variant bases) in distinct tracks and overlaid on associated data tracks. Mutations displayed in distinct tracks are color coded by type (missense, silent, and so on). Mutations overlaid on data tracks are colored black for clarity.

Use the Color Legends window to view or change the mutation color codes.

Use the Mutations tab of the Preferences window to modify other display options for mutations.