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
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 readsAt which point do I add read groups?
Thank you