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I'm wondering how to speed up picard's SortSam? It takes a long time to run it and I know GATK can be multi-threaded but I have not found example on Picard yet.

I'm wondering how other people tackle this problem?

zx8754
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jackyen_2000
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  • You might consider using samtools sort instead of Picard. You can use multiple CPU threads with samtools sort. – Steve Oct 30 '17 at 13:12

1 Answers1

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Unfortunately, sorting a random BAM file can't be speed up due to the nature of the problem. That's why the tool doesn't offer multithreading.

ABCD
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