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04-29-2010, 01:56 PM
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#1 |
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Member
Location: London Join Date: Jan 2010
Posts: 65
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Picard
Hello all,
I merged two ELAND export files by using samtools, but samtools flagstat shows that 191134982 in total 0 QC failure 0 duplicates 139825529 mapped (73.16%) 191134982 paired in sequencing 95567491 read1 95567491 read2 0 properly paired (0.00%) 115989136 with itself and mate mapped 23836393 singletons (12.47%) 0 with mate mapped to a different chr 0 with mate mapped to a different chr (mapQ>=5) Why it shows 0 properly paired? Couldn't run picard MarkDuplicates, thread exception: Exception in thread "main" java.lang.NullPointerException at net.sf.picard.sam.DiskReadEndsMap.remove(DiskReadEndsMap.java:87) at net.sf.picard.sam.MarkDuplicates.buildSortedReadEndLists(MarkDuplicates.java:289) at net.sf.picard.sam.MarkDuplicates.doWork(MarkDuplicates.java:126) at net.sf.picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:143) at net.sf.picard.sam.MarkDuplicates.main(MarkDuplicates.java:105) Any help? Many thanks. |
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04-29-2010, 02:58 PM
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#2 | ||
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Nils Homer
Location: Boston, MA, USA Join Date: Nov 2008
Posts: 1,285
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Quote:
Quote:
Send both to samtools-help@lists.sourceforge.net |
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07-15-2014, 05:45 AM
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#3 |
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Member
Location: GZ,China Join Date: Jun 2014
Posts: 42
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I got the same error. Have you solved your problem, bair or nilshomer?
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