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  • menenuh
    Junior Member
    • Jan 2010
    • 8
    #1

    Alignment statistics from bwa?

    Hello, I am a newbie and I have a question,
    Is it possible to get alignment statistics from sam output of bwa algorithm? And also, what happens to unaligned reads? Are there also present in the generated sam file? I have several 0's in the FLAG field in the sam output, is it an unmapped read?
    Well, it seems like I have more than one question
    Tags: None
    • lh3
      Senior Member
      • Feb 2008
      • 686
      #2
      You may get SAM output and then convert it to BAM. samtools flagstat will give you a brief stats. Unmapped reads are stored in the SAM file.

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