BAM

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.

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".  In both cases the index files must reside in the same directory as the BAM or SAM file.   Note: The "sai" index is an IGV format, it does not work with samtools or any other application.

Tools for sorting and indexing BAM files are available at the SAM Tools website referenced above.   SAM files can be sorted and indexed using the igvtools package.    

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.