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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
    Tags: samtools
    • 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 !

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