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  • samtools sorting outfile is not as large as input file

    I tried to sort a bam file for paired-end genomic data using samtools sort option. BAM file size is about 85gb. I sorted them on read names instead of chromosome coordinates. The output file is about 79gb. I am wondering where did 6gb of data from the input file go? Has anyone seen this type of inconsistency before?

    Thanks.

  • #2
    That's the magic of sorting a .bam; it comes out smaller, because it compresses better.

    If you do flagstat on the .bam before and after sorting, you'll see that they have the same number of reads.

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    • #3
      Definitely makes sure you have the right number of reads and that the sort did not prematurely terminate.

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      • #4
        Thanks a lot......... how would I know if the sorted file is complete?

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        • #5
          samtools flagstat or use samtools view -c to the count the reads

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