I had the same problem recently about adding the @RG group. You've probably solved it by now, but I'll leave this here for future searches (like the one I did for something else and this came up :) )

# Check if your BAM file has read group information:

samtools view -H .sorted.bam | grep '^@RG'

# If not, you can add them after the fact. https://gatk.broadinstitute.org/hc/en-us/articles/360035532352

gatk AddOrReplaceReadGroups --RGID test --RGLB --RGPL Illumina --RGSM --RGPU -I .sorted.bam -O .sorted.RG.bam

# You may need to re-index the new file

samtools index .sorted.RG.bam

#The following was adapted from https://www.biostars.org/p/365882/

####### REMOVING PCR DUPLICATES FROM YOUR BAM FILES

# Sort by name, rather than position

samtools sort -n -o namesort.bam example.bam

# Add ms and MC tags for markdup to use later

samtools fixmate -m namesort.bam fixmate.bam

# Markdup needs position order

samtools sort -o positionsort.bam fixmate.bam

# Finally mark duplicates. Use -r flag to remove duplicates, and -s to print stats.

samtools markdup positionsort.bam markdup.bam

Ed

Picard can mark duplicate for NGS data then you can remove duplicated reads after that. In addition, in GATK tool, if you run variant calling, after marked duplication, pipeline automatically remove those.

Command for mark duplicate with Picard:

java -jar picard.jar MarkDuplicates \ I=input.bam \ O=marked_duplicates.bam \ M=marked_dup_metrics.txt