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