Indel realignment GATK4

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David Lord

• November 18, 2021 10:44

Is there any way to run indel realignment on GATK4? I am aware that indel realignment is no longer necessary in the variant calling workflow of GATK4, however, I wish to perform further downstream analyses on my BAM files that requires indel realignment. 

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• Official comment

  

  Genevieve Brandt (she/her)

  • November 24, 2021 20:59

  Hi David Lord,

  There is no way to do indel realignment on its own in GATK4. You can read some of the logic behind this change at our legacy blog and forum site:

  • https://github.com/broadinstitute/gatk-docs/blob/master/blog-2012-to-2019/2016-06-21-Changing_workflows_around_calling_SNPs_and_indels.md?id=7847
  • https://sites.google.com/a/broadinstitute.org/legacy-gatk-forum-discussions/2016-04-07-2015-11-26/7131-Is-Indel-realignment-removed-from-GATK4
  • https://sites.google.com/a/broadinstitute.org/legacy-gatk-forum-discussions/2018-04-11-2017-12-02/11324-GATK4-realignment

  This request has already been posted to the GATK github. Feel free to add your use case and thoughts to the conversation to see if the work can get started again. Unfortunately, I do know our developers have many other projects going on, but it doesn't hurt to comment there.

  Best,

  Genevieve

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