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 taking too long
When I run the pipeline according to best practices, HC on a fastq of 60MB (for a targeted panel) takes about 10 minutes, but then for the same pipeline/targeted region, on a fastq of 150MB, HC takes 6 hrs. Any idea what would explain such a stark jump in runtime? Also, is there any way to reduce it? Can I use -Xmx -Xms arguments to increase the speed if memory is not an issue?
Any help will be appreciated.