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  • 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

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

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    • #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.

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

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