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  • jstjohn
    Member
    • Jun 2010
    • 35
    #1

    what is the new bwa sampe "prior of chimeric rate" option?

    Hey everyone,
    I am confused about what the new bwa sampe "prior of chimeric rate" option does, can anyone explain it to me? Thanks!
    -John
    Tags: None
    • jnfass
      Member
      • Aug 2008
      • 88
      #2
      Hey John! I'm looking for this as well ... did you ever get an answer from somewhere else? Specifically I think I'm seeing reduced (compared to alignments using bwa-0.5.8?) mapping qualities for paired reads that map to separate chromosomes ... was wondering if this parameter (and its default) have anything to do with that.

      ~Joe

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