Test-drive the GATK tools and Best Practices pipelines on Terra
Check out this blog post to learn how you can get started with GATK and try out the pipelines in preconfigured workspaces (with a user-friendly interface!) without having to install anything.
I'm getting an error "ERROR: Option 'RGID' cannot be specified more than once."
The command I use is:
picard -jar /path/to/picard.jar AddOrReplaceReadGroups I=/path/to/bam.bam O=/path/to/bam_rgs.bam RGID=0 RGLB=lib1 RGPL=illumina RGPU=unit1 RGSM=sample
If I remove RGID from the command, the error message says that RGID must be specified.
I'm using the Picard v. 2.12.1. I got the same error with v.2.9.2.