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  • thinkRNA
    Member
    • Jan 2010
    • 94

    #1

    convert BAM -> SAM?

    how can one convert from BAM to SAM
    I can use samtools to go from SAM to BAM but not other way. samtools only outputs BAM format, does anyone know? Thanks in advance!
  • lvaruzza
    Junior Member
    • Feb 2008
    • 8

    #2
    samtools -b -S in.sam > out.bam

    Comment

    • thinkRNA
      Member
      • Jan 2010
      • 94

      #3
      Originally posted by lvaruzza View Post
      samtools -b -S in.sam > out.bam
      is this not sam to bam? I want to go the other way (bam to sam). thanks!

      Comment

      • zee
        NGS specialist
        • Apr 2008
        • 249

        #4
        Read the samtools manual page at http://samtools.sourceforge.net/samtools.shtml

        samtools view in.bam > out.bam

        Comment

        • Daniel Su
          Junior Member
          • Jun 2010
          • 2

          #5
          Originally posted by zee View Post
          Read the samtools manual page at http://samtools.sourceforge.net/samtools.shtml
          Thank you zee.
          By the way, the header section would be absent.
          Last edited by Daniel Su; 06-30-2010, 03:14 AM.

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