BAM Similarity

Question

[rafi.schulman]

Hi all. I am curious if there are any tools to quantitatively compare the similarity of two BAM files. There are many documented methods for comparing similarity between two or more fasta files: simple sequence distance, phylogenetic approaches, so much more. However, I am interestedin ways to put a number on similairty of entire BAM files.

Obviously, I know there are many different ways of thinking about "similarity". I am open to any reasonable definition.

[GenoMax]

What is the use case you are thinking about here, if I may ask? Are these files related in some way?

Some suggestions: BAM file comparison and https://gatk.broadinstitute.org/hc/en-us/articles/360037593571-CompareSAMs-Picard-