I am running the AddOrReplaceReadGroups and do not know what to put for the items in bold. This is PE data from an Illumina NextSeq. The bam file name is long (I tend to name them with what has been done so far):
Thank you .
Code:
dedup_sorted_mapped_unmatched_adapter_removed_quality_trimmed_NA12878-NextSeq-S1_R1_and_R2.bam
Code:
# fix the read groups java -jar picard.jar AddOrReplaceReadGroups \ I= reads_without_RG.bam \ O= reads_with_RG.bam \ SORT_ORDER=coordinate \ [B]RGID=foo \ [/B] [B]RGLB=bar \[/B] [B]RGPL=illumina \ [/B] [B]RGSM=Sample1 \[/B] CREATE_INDEX=True
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