I also read this article. https://software.broadinstitute.org/gatk/blog?id=7847

However, i'm not clear why Indelrealignmnet Step is omitted.

In this article, i understand like that When using Mutect2 or Haplotypecaller, we do not need indel realignment.

But, i very confused when i use the tools that are not in gatk package(e.g Varscan2, CNVkit.. etcs)

If we do not use gatk tools, do we need indel realignment process?

i just really want to follow the data pre-processing workflow of GATK guideline. Thank you