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  • ElMichael
    Member
    • Jun 2009
    • 31
    #1

    BWA: suboptimal alignments

    Hi,
    I wonder is it possible for BWA to avoid search for suboptimal alignments? I want only equally best hits to be reported.
    And could I somehow limit the possible number of equally best hits that would be reported in X0 tag? It could be done for XA, but for X0... E.g., read1 could be equally mapped to the 100 positions. Will BWA report 100 in the X0?
    thanks!
    Last edited by ElMichael; 03-29-2011, 08:30 AM.
    Tags: None
  • lh3
    Senior Member
    • Feb 2008
    • 686
    #2
    you can write a simple script to filter the output.

    Comment

    • ElMichael
      Member
      • Jun 2009
      • 31
      #3
      Yes, I just thought that maybe there is a built-in option.
      And what is the upper limit for the parameter -n in samse (Maximum number of alignments to output in the XA tag)? I have one read that could be mapped equally good to 578 positions (at least so does X0 tag tell), but when I set -n 1000 I didn't get all these 578 alignments in XA tag.

      UPD: sorry, they are in sam file, they just were not parsed by my script.
      But anyway, is there any inherent limit for -n or not?
      Last edited by ElMichael; 03-29-2011, 01:34 PM.

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