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It's not finished yet, but I wanted to post this for discussion. In particular 7 of the 56 mark duplicates integration tests are failing with \"Cannot get mate information for an unpaired read\" - I'm not sure how to address that. I'd appreciate some help on this one.\r\n\r\nThe code currently has four shuffles: one groupBy in transformFragments (in MarkDuplicatesSparkUtils), two groupBys in transformReads, and one combine (foldByKey) in generateMetrics. The combine is more efficient than the others since it can run on the map side, reducing the amount of data that goes through the shuffle.\r\n\r\nI think it may be possible to merge the processing of the fragments and the reads to eliminate a shuffle - so there are only two shuffles for the main transform. A fragment would be represented as a pair with an empty second slot, so it can be handed in the processing separately from the true pairs that have both slots filled. 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