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  • Protaeus
    Member
    • Aug 2010
    • 21

    #1

    BWA: Is alignment summary available?

    Is there a tool associated with BWA that can provide a concise overall summary of the alignments/pairing, such as:
    1. How many reads did not map?
    2. How many single ends mapped?
    3. How many reads were successfully paired
  • swbarnes2
    Senior Member
    • May 2008
    • 910

    #2
    I don't think so. I use samtools flagstat.

    Comment

    • DZhang
      Senior Member
      • Jun 2010
      • 177

      #3
      I use picard

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