This site is now read-only. You can find our new documentation site and support forum for posting questions here.
Be sure to read our welcome blog!
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?