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.
can MuTect downsample a BAM file?
I noticed the latest version of MuTect provides these parameters: --downsampling_type, --downsample_to_fraction, and --downsample_to_coverage. So I wonder if MuTect can be used to downsample a BAM file. I would be thankful if you could provide more details of these parameters, e.g. example command line. Thanks in advance