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?