I have a bam file which is missing read groups in the header.
Picard ValidateSamFile.jar gives : ERROR: Record 1, Read name M0VN6:402:2486, RG ID on SAMRecord not found in header: M0VN6 ...
So I try to use Picard AddOrReplaceReadGroups:
AddOrReplaceReadGroups.jar I= myBam.bam O= myBam.readGroupReplaced.bam SORT_ORDER=coordinate RGID=myBam RGLB=myBam RGPL=IONTORRENT RGSM=myBam RGPU=myBam
This gives the error:
ERROR: Record 1, Read name M0VN6:402:2486, RG ID on SAMRecord not found in header: M0VN6 ...
Why does Picard AddOrReplaceReadGroups crash about this? This is what I am trying to fix by using that function. Or do I misunderstand what AddOrReplaceReadGroups does?
What I get from the AddOrReplaceReadGroups discription is that it replaces all read groups in the Bam file with the one specified and assigns all reads to this read group.