Your BAM header should have @RG read group entries that indicate the library sequenced (
LB:), the sample (
SM:), and the ID (
ID:). For example:
@RG ID:someid PL:illumina LB:H_IJ-NA19238-NA19238-lib1 SM:H_IJ-NA19238-NA19238
Additionally, library names should be unique across samples.
You should also be aware that BreakDancer expects that each read will be properly tagged indicating the read group is came from.