Test-drive the GATK tools and Best Practices pipelines on Terra
Check out this blog post to learn how you can get started with GATK and try out the pipelines in preconfigured workspaces (with a user-friendly interface!) without having to install anything.
Indel Realignment in Tumor-Normal pairs
Hello dear GATK team,
I have a question regarding indel realignment when doing somatic variant calling (tumor normal pairs). First of all, I am aware that indel realignment is not required by mutect2 but I am still using it for other somatic variant callers. There are a couple of papers mentioning that indel realignment should be done jointly (with both BAMs as input of the RealignerTargetCreator amd IndelRealigner). I tested this using simulated datasets and it did give better results.
I am interested in the reasoning for this, and is this something that should happen in general? In addition, I have a concern regarding differences in coverage. Would this method cause issues if there is a significantly higher coverage in a tumor sample to that in a normal sample?
Thanks in advance!