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  • Bruins
    Member
    • Feb 2010
    • 78
    #1

    Picard HsMetrics NEAR_BAIT_BASES interval

    Hi all,

    The Picard tool 'HsMetrics' collects metrics on hybrid selection. One of the colums in the output is 'NEAR_BAIT_BASES', defined as "The number of PF aligned bases that mapped to within a fixed interval of a baited region, but not on a baited region."

    Does anyone know how many bases the 'fixed interval' is?

    Source code of Picard 1.25 (we currently use 1.32) suggests this interval is 250 (the static NEAR_BAIT_DISTANCE attribute). Is this the number I'm looking for, or is my question waaaaaay too straightforward?

    Cheers
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