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  • sgroenewold
    Junior Member
    • Jan 2013
    • 4
    #1

    HS_LIBRARY_SIZE vs. ESTIMATED_LIBRARY_SIZE

    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?
    Tags: hsmetrics, markduplicates
    • Steve_DePalma
      Junior Member
      • Feb 2010
      • 1
      #2
      That has always been my understanding, yes.

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