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  • SquirrelSeq
    Member
    • May 2013
    • 10
    #1

    Show uncovered positions in pileup files

    Hello everyone,

    I created pileup files from sam/bam files via Samtools.

    For every reference in the alignment, the pileup entries start from the 5'-most reference position that is covered by reads.

    How can I force Samtools to list the uncovered positions too?

    Best regards,
    SquirrelSeq
    Tags: None
    • SquirrelSeq
      Member
      • May 2013
      • 10
      #2
      I know that Samtools is very common in NGS data analysis.

      So is my question confusing or not precise enough?

        Comment

        • mmanrique
          Member
          • Dec 2009
          • 12
          #3
          Hey, take a look at this thread

          http://seqanswers.com/forums/showthread.php?p=98872

          is this what you wanted to do?

            Comment

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