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.
Downsampling in GenotypeGVCFs
The documentation for GenotypeGVCFs states that it is employing downsampling:
This tool applies the following downsampling settings by default.
To coverage: 1,000
I also see this in my output :
"INFO 14:51:47,705 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000"
Specifically what is it downsampling, the genotype likelihoods per locus or active region? Is this behaviour changeable via -dcov, or would changing it be inadvisable?