How to compare alignments(SAM/BAM files) aligned to different references?

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I have two BAM files which are the output of alignments from two different references.

I want to compare two BAM files with some criteria in order to check the difference between the two references.

What is the appropriate way to compare the two alignments(references)?

(Tool suggestions, etc..)


sam


WGS


NGS


bam


alignment

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