Nothing came up on a search here today for me, so I dug into these Picard modules.
Looks like MarkDuplicates.ESTIMATED_LIBRARY_SIZE estimates the number of unique fragments supplied by the entire library, while HsMetrics.HS_LIBRARY_SIZE focuses only on the unique/duplicate reads aligned to the bait regions. Both use the Lander-Waterman equation to work backwards from unique reads vs. total reads.
Does that assessment agree with others here?
Looks like MarkDuplicates.ESTIMATED_LIBRARY_SIZE estimates the number of unique fragments supplied by the entire library, while HsMetrics.HS_LIBRARY_SIZE focuses only on the unique/duplicate reads aligned to the bait regions. Both use the Lander-Waterman equation to work backwards from unique reads vs. total reads.
Does that assessment agree with others here?
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