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  • mpileup format

    I am using samtools mpileup to analyze my data, and have several lines like this:

    chr1 14976 G 5 <<><> HHHHH
    chr1 14977 C 5 <<><> HHHHH
    chr1 14978 C 5 <<><> HHHHH
    chr1 14979 T 5 <<><> HHHHH
    chr1 14980 C 5 <<><> HHHHH
    chr1 14981 A 5 <<><> HHHHH
    chr1 14982 T 5 <<><> HHHHH
    chr1 14983 G 5 <<><> HHHHH
    chr1 14984 A 5 <<><> HHHHH


    What are those ">" "<" or "*" mean in the reads base column? According to the description of the format (http://samtools.sourceforge.net/pileup.shtml), they should be only in the base qualities columns.

  • #2
    samtools manual says they are " ’>’ or ’<’ for a reference skip".

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    • #3
      Originally posted by rnaseek View Post
      samtools manual says they are " ’>’ or ’<’ for a reference skip".

      http://samtools.sourceforge.net/samtools.shtml
      Thank u! This is really helpful!

      Comment


      • #4
        I am sorry to kick this thread alive but did someone figure out what "*" means in the reads base column? I cannot find any information on the homepage of Samtools.

        Comment


        • #5
          Originally posted by Rui View Post
          I am sorry to kick this thread alive but did someone figure out what "*" means in the reads base column? I cannot find any information on the homepage of Samtools.
          The deleted bases will be presented as ‘*’ in the following lines.

          Comment

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