MarkDuplicatesSpark error missing Read Group fields

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Field -Ye Tian

• October 09, 2020 16:45

If you are seeing an error, please provide(REQUIRED) :
a) GATK version used: 4.1.8.1
b) Exact command used: gatk MarkDuplicatesSpark -I input.bam -O output_duprm.bam --remove-sequencing-duplicates
c) Entire error log: 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

The above mentioned error occured. The sample I've been using is WES data, which I've aligned with BWA, and tranformed and sorted into .bam file with samtools. 

 

Thanks.

Field

1

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  Genevieve Brandt (she/her)

  • October 09, 2020 17:47

  Field -Ye Tian please see our documentation: https://gatk.broadinstitute.org/hc/en-us/articles/360035890671-Read-groups

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