Hi @wmsalsah
If you don’t know how the BAMs were constructed, start over with the reads for all samples.
Any intact BAM could have the fastq sequences extracted. Example tool: Operate on and transform BAM datasets in various ways
These tutorials can help with understanding fastq data (format/content/variants) along with example QA steps/tools. Also see domain/topic tutorials for protocol-specific QA steps.
There will be a training event in May that you might be interested in. You could get started with the Intro tutorials at any time, then work through the more advanced topics during.