MAF Mutation Files

MAF (mutation annotation format) files display mutations. IGV recognizes text-based files with .maf, .maf.txt  file extensions as mutation files. 

IGV will visualize each individual sample's mutation data as a single track.

• The all chromosomes view summarizes mutations in a coverage track (Screenshot below, 2015.02.18).
• Zooming in, individual chromosome views and more detailed views mark sites of mutations with open rectangles. Default settings display these in black-and-white.
• Color code mutations by mutation type (Screenshot above, 2015.02.18) by checking the Color code mutations box under View>Preferences>Mutations. See the Preferences page for more details.
• Mouse-over or click on a mutation to bring up an information panel on the specific mutation. This panel displays the information provided in the mutation file columns, in order, up to an area limit.
• A site where both alleles are mutated, or is mutated in multiple samples in a track that is a conglomerate of multiple samples, displays the rectangle with a horizontal line through the middle.