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read groups #10

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AnneJRomero opened this issue Dec 18, 2023 · 0 comments
Open

read groups #10

AnneJRomero opened this issue Dec 18, 2023 · 0 comments

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@AnneJRomero
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Hi,

I am trying your variant_calling.sh for GATK pipeline.

I got the error below:

A USER ERROR has occurred: Bad input: Sam file header missing Read Group fields. MarkDuplicatesSpark currently requires reads to be labeled with read group tags, please add read groups tags to your reads

At which point do I add read groups?

Thank you
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@AnneJRomero