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.
Dream challenge PON
The Supplementary Data for the Dream challenge (http://www.nature.com/nmeth/journal/v12/n7/full/nmeth.3407.html) indicates that a panel of normals filter was used for the Broad's Mutect submission:
"Panel of normals filter:
matlab: survey_panel_of_normals_for_mutations(maf_file, bamfile_list.txt) where bamfile_list.txt contains 258 normal whole genome bam files to use as an additional panel of normals."
Is this dataset available to the public?