Genome Analysis Toolkit

Variant Discovery in High-Throughput Sequencing Data

GATK process banner

Need Help?

Search our documentation

Community Forum

Hi, How can we help?

Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools with a primary focus on variant discovery and genotyping. Its powerful processing engine and high-performance computing features make it capable of taking on projects of any size. Learn more

Read groups: How do I assign RGID when all samples in a pool are run on all available lanes on a flow cell?



  • Avatar
    Genevieve Brandt (she/her)

    ISmolicz each ID must be unique for each read group, it does not necessarily need to be named with the flowcell. 

    For example, this read group:

    @RG ID:H0164.2  PL:illumina PU:H0164ALXX140820.2    LB:Solexa-272222    PI:0    DT:2014-08-20T00:00:00-0400 SM:NA12878  CN:BI


    Comment actions Permalink
  • Avatar

    Thank you for confirming Genevieve Brandt. I will ensure the RGID is unique per read group.

    Comment actions Permalink

Please sign in to leave a comment.

Powered by Zendesk