I'm looking for official algorithm documentation on Picard MarkDuplicates and SamTools rmdup, but I can't find it. I have found numerous posts in "google land" where people state why one is better, but I want to know exactly how they both work (preferably without going through the code). For example, I have "heard" that MarkDuplicates is more "intelligent" because it allegedly considers variants within a read rather than just looking at where reads begin.
Can anyone point me towards a paper or documentation that discusses the true differences between the algorithms?
Thanks for your help!