It seems like your BAM contained sequencing reads! This is what is expected.
From here, you can do things like:
- assemble the reads into contigs (consensus sequences based on read evidence)
- compare the reads to known genomes to identify variants
- classify the reads against known species
For your question here:
This falls into an assembly protocol. The topics at this forum with the assembly tag are good reasources. One prior topic is here:
Please give that a review and let us know if we can help more! Later on, should you run into tool issues, you can start up new topics for community help.