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.
We are running GATK v2.4.9 and are calling SNPs and indels with Unified genotyper (multi-sample calling) followed by variant recalibration. We noticed that the best practices does not recommend masking out the indel calls for the samples before calling SNPs, is this no longer necessary because of VQSR?