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.
Window size for samples of varying coverage
The documentation of the CNVDiscoveryPipeline makes it clear that several run parameters should be adjusted based on sequencing coverage. My samples are of variable coverage, but generally fall into 3 bins: ~25% are ~50x, ~25% are ~25x, and the remainder are ~10x coverage. We have about ~400 remaining samples that we intend to sequence to ~10x.
I'm wondering what peoples' thoughts/experiences are with setting window size for a set of samples with variable coverage. I considered setting parameters based on the average coverage across samples, but this may not be optimal for any particular sample. I also considered using optimal parameters for the high coverage samples (smaller windows), which would sacrifice processing time for sensitivity, if I'm reading the documentation correctly. However, it sounds like window sizes that are too small will also reduce sensitivity, in the extreme. If I set parameters with respect to my high coverage samples (30-50x), would these parameters be considered extremely too small for samples at 10x?