I'm trying to call variants from multiple samples at once with high coverage using UnifiedGenotyper. In this sense, I set the -dcov parameter in a few thousands reads by position. However, using such a strategy, GATK takes too much time. As far as I know, -dcov is a way for downsampling, but I don't know if such a downsampling is random or implies just the first reads for a given position. Perhaps using -dfrag option could be a right way to randomly downsampling multiple samples highly covered??
Thank you very much for your help!