I'm brand new in Bioinformatics, and building my first variant calling pipeline for human genomes. Now, I got stuck using BaseRecalibrator as it needs read groups in my .bam file, so I took my
sorted_dedup_output.bam and ran Picard AddOrReplaceReadGroups.
Is it necessary for me to reapply a sorting and duplicate marking step? Thanks in advance! Very helpful community!