MarkDuplicatesSpark error missing Read Group fields
If you are seeing an error, please provide(REQUIRED) :
a) GATK version used: 126.96.36.199
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.
Field -Ye Tian please see our documentation: https://gatk.broadinstitute.org/hc/en-us/articles/360035890671-Read-groups
Please sign in to leave a comment.