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.
Is it OK to stack IndelRealigner runs
Hi GATK Team,
My question is related to whether it is OK to run IndelRealigner twice on the same .bam file, first individually, and next with its tumor or normal pair. This seems to be what's recommended in the PPT on the google drive titled "Somatic Variant Discovery"
but I wanted to double-check because I also read that IR modifies the mapping quality of reads that it realigns, which might affect the next IR run. Any insight would be much appreciated. Thanks so much.