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.
Use all samples or group samples for GenotypeGVCFs?
I have created g.vcfs for all my samples (48). Half of my samples (24) are control individuals and the other half (24) is treated individuals. Should I run
GenotypeGVCFs on all my samples once to generate one raw vcf? Or twice, once for treated samples and once for control samples producing two raw vcfs? Ultimately I am looking for differences between my groups.