From Genome Analysis Wiki
==== Bam Format ====use .bam extension to output in BAM format instead of diff format.
In BAM format there will be 3 output files:
# the specified name with record diffs
# specified name with _only_<in1>.
bam with records only in the in1 file# specified name with _only_<in2>. bam with records only in the in2 file
When a record is found in both input files, but a difference is found, the record from the first file is written with additional tags to indicate the values from the second file, using the following tags: