RGID versus RGPU

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Jean-Michel Carter

• October 20, 2022 06:49
• Edited

Hello! I am facing some confusion regarding RGID and RGPU when correcting read groups using AddOrReplaceReadGroups.

Your documentation (here and here) appears to imply that RGPU {FLOWCELL}.{LANE}.{LIBINDEX} is optional however the current AddOrReplaceReadGroups has the RGPU field as a mandatory argument while the RGID {FLOWCELL}.{LANE} is optional.

Additionally there is some external documentation that appears to recommend making the RGID similarly to the RGPU you described {FLOWCELL}.{LANE}.{LIBINDEX} while the RGPU is more similar to the RGID you described: {FLOWCELL}.{LANE}.

Could you clarify then wether we should be defining read groups containing unique RGPUs {FLOWCELL}.{LANE}.{LIBINDEX} and some shared RGIDs {FLOWCELL}.{LANE} OR should it be unique RGIDs {FLOWCELL}.{LANE}.{LIBINDEX} and shared RGPUs {FLOWCELL}.{LANE}?

GATK version used: 4.3.0.0
Exact command used: AddOrReplaceReadGroups

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  Genevieve Brandt (she/her)

  • October 21, 2022 18:56

  Thank you for your post, Jean-Michel! I want to let you know we have received your question. We'll get back to you if we have any updates or follow up questions. 

  Please see our Support Policy for more details about how we prioritize responding to questions. 

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