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  • Picard with SMALT?

    Has anyone ever tried to use Picard tools with SMALT? Specifically AddOrReplaceReadGroups and MarkDuplicates. Here is the error I get when trying to add read groups:

    Code:
    [Thu Apr 19 16:26:33 EDT 2012] Executing as gareth@farin on Linux 3.0.0-17-generic amd64; OpenJDK 64-Bit Server VM 1.6.0_23-b23; Picard version: 1.65(1160)
    INFO	2012-04-19 16:26:33	AddOrReplaceReadGroups	Created read group ID=foo PL=illumina LB=bar SM=GARETH
    
    [Thu Apr 19 16:26:33 EDT 2012] net.sf.picard.sam.AddOrReplaceReadGroups done. Elapsed time: 0.00 minutes.
    Runtime.totalMemory()=1901723648
    FAQ:  http://sourceforge.net/apps/mediawiki/picard/index.php?title=Main_Page
    Exception in thread "main" java.lang.IllegalArgumentException: No enum const class net.sf.samtools.SAMFileHeader$SortOrder.unknown
    	at java.lang.Enum.valueOf(Enum.java:214)
    	at net.sf.samtools.SAMFileHeader$SortOrder.valueOf(SAMFileHeader.java:59)
    	at net.sf.samtools.SAMFileHeader.getSortOrder(SAMFileHeader.java:240)
    	at net.sf.picard.sam.AddOrReplaceReadGroups.doWork(AddOrReplaceReadGroups.java:87)
    	at net.sf.picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:177)
    	at net.sf.picard.cmdline.CommandLineProgram.instanceMainWithExit(CommandLineProgram.java:119)
    	at net.sf.picard.sam.AddOrReplaceReadGroups.main(AddOrReplaceReadGroups.java:61)

  • #2
    Are you trying to sort as well? Without sorting, picard worked for my Smalt bams.
    picard => samtools sort =>

    Comment


    • #3
      I think I have encountered this problem - if I remember correctly I think the problem is that SMALT puts "unknown" as the value for the SO tag and that this value is not allowed by Picard. I think it worked fine after I changed these tags.

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