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Samtools sort vs Picard Sortsam

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  • dpryan
    replied
    Originally posted by swbarnes2 View Post
    I think Picard's sortSam puts a line in the header indicating that the file is sorted, which samtools does not. But for lots of applications this doesn't matter.
    Are you sure about that? The header is grabbed from the first tmp file written.

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  • swbarnes2
    replied
    I think Picard's sortSam puts a line in the header indicating that the file is sorted, which samtools does not. But for lots of applications this doesn't matter.

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  • sklages
    replied
    So if you get the same results in terms of mem and runtime for huge files, just decide for the one you're more familiar with. Edge cases are usually very specific, so if you don't encounter any problems with your regular files, no need to worry :-)

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  • ymc
    replied
    Originally posted by sklages View Post
    Why don't you just try?
    Because they give the same results after I try. I think there might be differences in edge cases, for example, when it is piped from bwa-mem. But I don't know what the edge cases are.

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  • sklages
    replied
    Why don't you just try?

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  • ymc
    replied
    I want to know SortSam vs samtools sort, too.

    I think MarkDuplicates is better than rmdup because the former can handle duplicates across break points.

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  • rahul
    started a topic Samtools sort vs Picard Sortsam

    Samtools sort vs Picard Sortsam

    Hi all,

    Which is a better pick for sorting large SAM files in terms of memory requirement and run time: sortSam from Picard or Samtools sort function. Could you please direct me to the thread if it is already discussed and i missed it.

    Thank you,

    Rahul
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