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  • bam files not sorted by samtools sort

    Hi,

    Could I please be adviced on the following problem. I have sam files generated from bismark. I converted it to bam file using samtools view and sorted it by coordinates using samtools sort. When I checked the header of both the sorted and unsorted bam files, they both stated the files are unsorted.

    I am unsure why this would be the case.

    Would anyone be able to shed light on this issue?

    Thanks

  • #2
    Which version of samtools did you use? Older versions never bothered to update the header (but still sorted the reads).

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    • #3
      I am using version 0.1.18. I am now certain that the files had not been sorted. I ran the files through our downstream analysis programs which threw an error indicating the flies were unsorted.

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      • #4
        The best test if a BAM file is sorted is to try "samtools index your_file.bam", if that works the file is coordinate sorted.

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