Picard MergeSamFile Memory Increase

qqcandy

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Join Date: Sep 2008

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Picard MergeSamFile Memory Increase

07-14-2010, 06:00 AM

Does anyone know how I can increase the memory allowance of Picard MergeSamFile? The current one always use around 2 to 3G, no matter how much memory the machine actually has... And I can't find any parameter in Picard MergeSamFile that control the memory...

Wondering whether MergeSamFile is faster with more than 3G memory too...

Thanks!
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drio

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Join Date: Oct 2008

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07-14-2010, 06:32 AM

Pass -Xmx XG to your virtual machine where XG is the amount of memory you want
to use.

Also, use the multithreading option (USE_THREADING=Boolean) that has been recently added to picard. That should increase the performance by 20% (From the picard docs).

-drd
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