Add read group to bam

[cmccabe]

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):

dedup_sorted_mapped_unmatched_adapter_removed_quality_trimmed_NA12878-NextSeq-S1_R1_and_R2.bam

# 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

Thank you .

[dpryan]

They can all be whatever you want. I tend to use the same thing for SM, ID and LB, which works unless you make multiple libraries from samples or run them at multiple times. PL is fine as "illumina".

[cmccabe]

This is one library, but in the future they will be barcoded. I am new to Illumina data and getting used to it. Thank you .

   RGID=NextSeq \     (identifier)
   RGLB=IDP \            (library method)
   RGPL=illumina \      (platform)
   RGSM=NA12878 \   (sample)

[GenoMax]

@Devon: Do you always use them? They are not strictly needed (except GATK tools, are there other programs?).

[Bukowski]

@Devon: Do you always use them? They are not strictly needed (except GATK tools, are there other programs?).

I thought GATK was the entire reason AddOrReplaceReadGroups existed

[cmccabe]

I went ahead and tried the below and get a RGPU required error but there is no mention of that on the GATK website. Thank you .

cmccabe@DTV-A5211QLM:~/Desktop/NGS$ java -jar /home/cmccabe/Desktop/NGS/picard-tools-1.139/picard.jar AddOrReplaceReadGroups \
> I=/home/cmccabe/Desktop/NGS/picard-tools-1.139/dedup_sorted_mapped_unmatched_adapter_removed_quality_trimmed_NA12878-NextSeq-S1_R1_and_R2.bam \
> O=/home/cmccabe/Desktop/NGS/picard-tools-1.139/RG_dedup_sorted_mapped_unmatched_adapter_removed_quality_trimmed_NA12878-NextSeq-S1_R1_and_R2.bam \
> SORT_ORDER=coordinate \
> RGID=NextSeq \
> RGLB=IDP \
> RGPL=illumina \
[B]> RGPU=R1 \[/B]
> RGSM=NA12878 \
> CREATE_INDEX=True
ERROR: Option 'RGPU' is required.

Edit: I added the RGPU as R1 (FASTQ files were all labled R1_S1 or R1_S2, so I figured R1 was the lane and the S1 or S2 referred to the diirection)

[Bukowski]

https://broadinstitute.github.io/picard/command-line-overview.html

RGPU (String) Read Group platform unit (eg. run barcode) Required.

[GenoMax]

I thought GATK was the entire reason AddOrReplaceReadGroups existed

It does feel like it since that is the only time I have used that tool.

[cmccabe]

Thank you

[dpryan]

@Genomax: Our mapping pipeline automatically adds them, since Picard will bork (or at the very least complain) occasionally without them too. When I need to manually do the alignment I never add them...unless I need to use GATK :P

@cmccabe: One warning about using "NextSeq" as the ID is that the ID is the only value that MUST be unique when you compare multiple BAM files. Just keep that in mind before you get in the habit of assigning RGID.

[cmccabe]

Good to know... thank you very much .