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.
Print BAM file downsampled to coverage at given loci
I'm trying to print a bam file downsampled to a certain coverage at given loci. What I've tried thus far is to use PrintReads with -dcov XXX, but as the documentation states, it will downsample to that coverage based on the beginning of the aligned read. Is there a way to get a bam file that has been downsampled to a (nearly) precise coverage at specified loci?
I am not using GATK to call variants or any other purpose, so I can't do it while calling variants.
Thanks for your help!