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.
RealignerTargetCreator and IndelRealigner
The tools RealignerTargetCreator and IndelRealigner are obsolete in GATK4. Are there any replacements for these tools in GATK4?
Also, there are two option -BQSR (used with PrintReads) and -stand_emit_conf (used with HaplotypeCaller) that are not available with GATK4. What should be done in these cases?