How to extract best-hit reads from merged sam file with multiple hits per read?
I have multiple sam files that I would like to merge. The only problem is that I may have instances where there will be multiple hits per read.
Is there a way to use sam tools or any other software for removing these “duplicate” hits based on some criteria such as highest score?
Also, my usage of “duplicate” is referring to multiple hits for a read since I am merging sam files.
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