VCF (variant call format), MAF (mutation annotation file), and MUT (mutation) file formats display variations in sequence. Here we refer to MAF and MUT files together as mutation files. Links above take you to details for each format in the File Formats guide. Links below detail visualizing each type of file on IGV.
As tracks, MAF and MUT files display in a similar manner and you can overlay each on other data tracks so long as sample names follow TCGA conventions or match. To overlay all other MUT and MAF files, you must use a linking identifier in a sample information file as described in Mutation Files, and indicate this linking identifier in the Mutations Preferences Panel.