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  • Picard CalculateHsMetrics Function - what do all the output abbreviations mean?

    Hi,

    I am using the CalculateHsMetrics in Picard to estimate the per cent of on and off target reads for some next generation sequence data that I am aligning against a reference genome. I am running Picard via the Galaxy server (usegalaxy.org/).

    I am having trouble understanding some of the program outputs. A list of my specific queries is given below. Any advice anyone can give me would be greatly appreciated.


    What do the following outputs stand for?
    PF_READS
    PF_UQ_READS_ALIGNED 5403054
    PCT_PF_UQ_READS_ALIGNED
    PF_UQ_BASES_ALIGNED
    ON_BAIT_BASES
    ON_BAIT_VS_SELECTED
    FOLD_ENRICHMENT
    ZERO_CVG_TARGETS_PCT
    FOLD_80_BASE_PENALTY
    HS_PENALTY

    I am also unsure about exactly what these outputs refer to:
    BAIT_TERRITORY and TARGET_TERRITORY - are these references to the total number of base pairs captured by the baits and targets?
    NEAR_BAIT_BASES - how near the baits are these bases? I understand that they cover a 250bp interval around each target or bait. Is this what the output is referring to?
    PCT_SELECTED_BASES - does this refer to the percent of the referene genome captured by the targets or baits?
    OFF_BAIT_BASES vs NEAR_BAIT_BASES - does the count of off-target bases include those bases that are near the baits/targets?

  • #2
    refer to this page http://picard.sourceforge.net/picard...html#HsMetrics

    Comment


    • #3
      Thank you ersgupta, much appreciated.

      Comment

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