As others have said, a bam file is a file containing alignments of raw sequencing reads. BreakDancer takes a bam file as input and discovers breakpoints of structural variants. The table you have is the result of running an algorithm like BreakDancer on sequencing data. That table already has a "variant class" column which tells you whether the event is a duplication or deletion. Their raw data is probably deposited in dbGaP or elsewhere, and you could download it and run BreakDancer or another algorithm on the data to try to recreate their results, but those are large files and that's a significant undertaking. - Chris Miller