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Which Read Groups are correct:

java -Xmx4G -jar picard.jar AddOrReplaceReadGroups \
I=$SNIC_TMP/WCRO84_S23_L005.bam \
O=WCRO84_S23_L005.bam \
RGID=WCRO84_S23_L005 \
RGLB=WCRO84 \
RGPL=illumina \
RGPU=WCRO84_S23_L005 \
RGSM=WCRO84

or

java -Xmx4G -jar picard.jar AddOrReplaceReadGroups \
I=$SNIC_TMP/WCRO84_S23_L005.bam \
O=WCRO84_S23_L005.bam \
RGID=WCRO84_S23_L005 \
RGLB=WCRO84_S23_L005 \
RGPL=illumina \
RGPU=WCRO84_S23_L005 \
RGSM=WCRO84_S23_L005

Or is a better way to determine read groups?

Thank you in advance,

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1 Answer 1

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Usually it doesn't actually matter, but if you want it to be very correct:

RGID=SomeLibraryID \
RGLB=SomeLibraryID \
RGPL=illumina \
RGPU=Some_Sequencer_ID \
RGSM=SomeSampleID

That assumes you have one library per sample and aren't splitting the output BAM files by lane.

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2
  • $\begingroup$ Is it possible to get it automatically determine by reading the FASTQ header or filename? $\endgroup$
    – user977828
    Commented Feb 18, 2019 at 13:16
  • $\begingroup$ If you have control of how the data is produced then yes, you can set all of that automatically. Otherwise you can't be certain the file/read names are meaningful. $\endgroup$
    – Devon Ryan
    Commented Feb 18, 2019 at 13:18

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