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.
Best practices for ContEst for WGS
What are the best practices for ContEst as far as the population file and interval list parameters go? I would imagine that interval list should be irrelevant when looking across the whole genome, but this seems to be a required argument.
I'm currently using /xchip/cga/reference/hg19/hg19_population_stratified_af_hapmap_3.3.vcf for the population file -- is that appropriate for WGS?
Thanks for the advice,