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.
what interval files do you guys use for human exome variant calling?
I downloaded my intervals files from UCSC human exome captured file (hg19_exome_sorted.bed), but I keep getting lots of "./." in the final VCF files. I asked before in this forum, and I remember Geraldine said this may be because of sub-optimal interval files. This made me wonder what you guys use for human exome variant calling?