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.
possible bug in GATK3.7
I started the variant filtration step with GATK 3.7 (see attached file and got immediately an error message). I switched to the version 3.6 and used the exact command line and it worked. So probably there is a bug in 3.7 or my vcf file is corrupt (created by UnifiedGenotyper). I searched for the string "18.78" in my vcf file and I found it in the first data line "...;QD=18.78;...."