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Thread | Thread Starter | Forum | Replies | Last Post |
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#1 |
Member
Location: canada Join Date: Sep 2009
Posts: 29
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Hey folks,
I'm trying to run markduplicates on some massive files (merged Solid bams), and often 100Gigs of RAM doesn't get the job done. Does anyone have a good suggestion for a workaround. I don't want to split into chromosomes because I lose the ability to mark dups that span multiple chromosomes. thanks! |
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#2 |
Senior Member
Location: WashU Join Date: Aug 2010
Posts: 116
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Is the BAM file sorted already? If not, is it possible that it is during sorting that picard uses excessive memory? If that's the case, you could, presort the BAM file using SAM tools (which allows max memory usage to be specified) and then use picard to mark duplicates using the 'ASSUME_SORTED' option...
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#3 | |
Senior Member
Location: 41°17'49"N / 2°4'42"E Join Date: Oct 2008
Posts: 323
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-drd |
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Tags |
bam, duplicates, picard |
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