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 still needed for GenomeSTRiP?
Indel Realignment is no longer a recommended best practice step for the GATK pipeline to call genotypes with HaplotypeCaller.
However, doesn't indel realignment still need to be run to prepare bams for GenomeSTRiP and many other SV callers that do not use haplotype assembly?