Answers.Body: <p>Usually it doesn't actually matter, but if you want it to be very correct:</p>
  
  <pre><code>RGID=SomeLibraryID \
  RGLB=SomeLibraryID \
  RGPL=illumina \
  RGPU=Some_Sequencer_ID \
  RGSM=SomeSampleID
  </code></pre>
  
  <p>That assumes you have one library per sample and aren't splitting the output BAM files by lane.</p>
  
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2019-02-18T13:16:43.677Z
Answers.Text: Is it possible to get it automatically determine by reading the FASTQ header or filename?
Answers.UserDisplayName: user977828
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2019-02-18T13:18:12.357Z
Answers.Text: 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.
Answers.UserDisplayName: Devon Ryan
Answers.ContentLicense: CC BY-SA 4.0
Answers.CreationDate: 2019-02-18T11:33:19.420Z
Answers.LastActivityDate: 2019-02-18T11:33:19.420Z
Answers.UserDisplayName: Devon Ryan
Body: <p>Which Read Groups are correct:</p>
  
  <pre><code>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
  </code></pre>
  
  <p>or</p>
  
  <pre><code>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
  </code></pre>
  
  <p>Or is a better way to determine read groups?</p>
  
  <p>Thank you in advance,</p>
  
Tags: <phylogenetics><sam><bwa><picard>
Title: Determining Read Groups
ThreadText: # Determining Read Groups
  
  (Asked by: username_0 on 2019-02-18)
  
  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,
  
  **Tags:** phylogenetics, sam, bwa, picard
  
  
  ---
  
  ## 1 answers
  
  ### Answer by username_1 on 2019-02-18. Score: 4
  
  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.
  
  > **Comments:**
  > **username_0**: Is it possible to get it automatically determine by reading the FASTQ header or filename?  
  > **username_1**: 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.  
  
  ---
  
  