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.
Phasing SNPs and Indels
I was looking into tools for phasing indels and SNPs. It seems that ReadBackPhasing only supports phasing of SNPs. I'm working on data from TCGA, and according to your docs HaplotypeCaller which can produce phased output, is not recommended for tumor samples. Is there any work around for this problem? Can MuTect phase the variants?