A BAM file is the binary version of the Sequence Alignment/Map (SAM) format, specification available at SAMTools site,  developed by the Data Processing Subgroup as part of the 1000 Genomes Project. 
Indexing: BAM files should be sorted by position and indexed prior to running Syzygy. Sorting and Indexing can be completed with SAMTools. 
Chromosome Names: Chromosome names must be consistent between .tgf files and BAM files.