BQSR --use-original-qualities

Follow

Alijah O'Connor

• April 20, 2020 22:02
• Edited

When looking at the GATK processing for variant discovery WDL script, I noticed that the Broad team use the parameter --use-original-qualities in both of the BQSR steps.  Why is this the case?  Wouldn't we want to keep the new recalibrated base qualities in most cases?

0

• 

  Bhanu Gandham

  • April 22, 2020 17:31

  Hi ,

  The GATK support team is focused on resolving questions about GATK tool-specific errors and abnormal results from the tools. For all other questions, such as this one, we are building a backlog to work through when we have the capacity.

  Please continue to post your questions because we will be mining them for improvements to documentation, resources, and tools.

  We cannot guarantee a reply, however, we ask other community members to help out if you know the answer.

  For context, check out our support policy.

   

  0

  Comment actions Permalink

Please sign in to leave a comment.