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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
    Tags: None
    • swbarnes2
      Senior Member
      • May 2008
      • 910
      #2
      I don't think so. I use samtools flagstat.

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        • DZhang
          Senior Member
          • Jun 2010
          • 177
          #3
          I use picard

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