How can I extract all known mutations of my BAM (or SNP/INDL files)?
If you have a BAM file, you could easily run a variant caller analysis software such as freebayes, though you would need a good amount of computing power like a cluster or a dedicated node with good memory. Freebayes outputs a vcf file that has all the variants listed. Then you can load it into the UCSC or Ensembl human genome browsers and look at what genes they are.