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.
HaplotypeCaller on 2000 samples, feasible?
I have previously tested HaplotypeCaller (GATK 2.7) on 100 samples. It takes a long time to run compared to UnifiedGenotyper. Is it feasible to use HaplotypeCaller on 2000 samples? Can I make it run faster other than by using multi-threading? Would it be an advantage for me to run ReduceReads prior to variant calling? I know the details are sparse, but I currently do not have any additional information. Thank you.