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MergeBAM RG ID and SM tags
Dear GATK team,
I have gone through the discussion on Merging lane wise bam and still I have little confusion.
Does it make difference if we have same RG ID and SM tags across all lanes as it was mentioned that MarkDuplicates will consider the library (flowcell)?
What if we have same sample lanes sequenced in more than one flowcell. How Markduplicates handled such cases? How does it affect on variant calling?
Please help me to resolve this type of cases.
Thanks In Advance