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  • Sylphide
    Member
    • Feb 2011
    • 11

    #1

    Samtools sort output smaller than input

    Hello,
    I have a problem with samtools sort : my output files are smaller than my input files when they should be identical since only the lines order is changed !
    Does anyone know this problem and a solution ?
    thanks
  • jkbonfield
    Senior Member
    • Jul 2008
    • 146

    #2
    It is correct and is caused by higher compression ratios from zlib when data is sorted.

    Comment

    • swbarnes2
      Senior Member
      • May 2008
      • 910

      #3
      Right, this is normal. You can confirm that yourself by running flagstat on the unsorted and sorted file. They will have the same number of reads.

      Comment

      • Sylphide
        Member
        • Feb 2011
        • 11

        #4
        Indeed they have the same read number.
        Many thanks for your help !

        Comment

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