To load a set of BAM files merged into a single track see Merged BAM File.
A BAM file (.bam) is the binary version of a SAM file. A SAM file (.sam) is a tab-delimited text file that contains sequence alignment data. These formats are described on the SAM Tools web site: http://samtools.sourceforge.net.
BAM, rather than SAM, is the recommended format for IGV. Starting with IGV 2.0.11, IUPAC ambiguity codes in BAM files are supported.
Indexing: IGV requires that both SAM and BAM files be sorted by position and indexed, and that the index files follow a specific naming convention. Specifically, a BAM index file should be named by appending .BAI to the bam file name. A SAM index filename is created by appending .SAI.
Chromosome names: Chromosome names must be consistent across all annotation and data files. For convenience, IGV equates chromosome numbers and names of the form chr# (e.g., 1 and chr1 are equivalent).
One-based index: Start and end positions are identified using a one-based index. The end position is included. For example, setting start-end to 1-2 describes two bases, the first and second in the sequence.