I have incomplete readgroups in some bam-files, and tried to update them using the recomended script from the tutorial;
java -jar $PICARD_JAR AddOrReplaceReadGroups \
I= /work/users/ED-Sam.sorted.bam \
O= /work/users/ED-Sam_newRG.sorted.bam \
RGID=IDEDSAM \
RGLB=lib1 \
RGPL=illumina \
RGPU=BH3NTKALXX.8.3 \
RGSM=IDEDSAM \
SORT_ORDER=coordinate \
CREATE_INDEX=true
I get this error Message (have tested two different Version of Pickard (1.139 and 2.10.3), both gives the identical error:)
`
Exception in thread "main" htsjdk.samtools.SAMFormatException: Error parsing SAM header. @RG line missing SM tag. Line:
@RG ID:EDSAM PL:ILLUMINA; File /work/users/ED-Sam.sorted.bam; Line number 3270
at htsjdk.samtools.SAMTextHeaderCodec.reportErrorParsingLine(SAMTextHeaderCodec.java:237)
at htsjdk.samtools.SAMTextHeaderCodec.access$200(SAMTextHeaderCodec.java:43)
at htsjdk.samtools.SAMTextHeaderCodec$ParsedHeaderLine.requireTag(SAMTextHeaderCodec.java:319)
at htsjdk.samtools.SAMTextHeaderCodec.parseRGLine(SAMTextHeaderCodec.java:167)
at htsjdk.samtools.SAMTextHeaderCodec.decode(SAMTextHeaderCodec.java:100)
at htsjdk.samtools.BAMFileReader.readHeader(BAMFileReader.java:503)
at htsjdk.samtools.BAMFileReader.(BAMFileReader.java:166)
at htsjdk.samtools.BAMFileReader.(BAMFileReader.java:125)
at htsjdk.samtools.SamReaderFactory$SamReaderFactoryImpl.open(SamReaderFactory.java:258)
at picard.sam.AddOrReplaceReadGroups.doWork(AddOrReplaceReadGroups.java:94)
at picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:206)
at picard.cmdline.PicardCommandLine.instanceMain(PicardCommandLine.java:95)
at picard.cmdline.PicardCommandLine.main(PicardCommandLine.java:105)
Suggestions?