PICARD replace group error

[mstagliamonte]

... not yet another read group thread...

Hi, everybody,

I am trying to set up a GATK analysis. I have two strains of the same microorganism, one MiSeq run (one lane) with one sample per strain. Total: 2 samples (multiplexed)

I got the demultiplexed files from the machine, mapped them with BWA-MEM, then run PICARD sortsam --> Picard mark duplicates --> now trying to run Picard AddOrReplaceReadGroups.

The error I am obtaining is: ERROR: Unrecognized option: RGID
My Picard version: 1.80
Let's go through my command line:

java -jar $HPC_PICARD_DIR/MarkDuplicates.jar INPUT=STRAIN_1.bam OUTPUT=STRAIN_1_OUT.bam RGID=miseq_run1 RGLB=illumina_STRAIN_1 RGPL=illumina RGPU=A58U1 RGSM=STRAIN_1 RGCN=miseq_Acq_pat RGDT=130918

For what I understand, both samples should be the same read group, as they originated from the same run, single lane. Am I correct?

The PICARD overview presents RGID=string, so I should be able to actually choose a name for the read group. But then presents the default = 1, and may be set = null.
( http://picard.sourceforge.net/comman...laceReadGroups )

Maybe I need to use a numeric identifier? Would that be the same for both samples in this case?
Please help a 'special' student

Thanks,
Max