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.
New representation in VCF (Genotype GVCF bug fix from v3.4) and downstream annotation
I am using GATK3.5 and I can see the new IUB <*:DEL> representation to accomodate the SNPs in the spanning deletions in a region. But this hinders the downstream annotation. Do you guys recommend a specific annotator that takes this new representation into consideration?