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 Picard Fixmate necessary ?
I recently used GATK, the latest version to carry out Indel realignment for my bam files. I have read at few places that one needs to fix the mate position information as the reads mapping position may change during realignment. My question is that does this step is taken care of y GATK automatically or one needs to run Picard fixmates before going for subsequent analysis.