The frontline support team will be slow on the forum because we are occupied with the GATK Workshop on March 21st and 22nd 2019. We will be back and more available to answer questions on the forum on March 25th 2019.
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?