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.
Joint Genotyping calling on different coverage samples
I'm using your Joint Genotyping protocol to detect variants on a cohort-wide analysis.
Initially I had 12 samples sequenced at ~ 50x but I had received a new batch of 20 samples sequenced only at 5x.
I was wondering if the recommended protocol should be to execute the GenotypeGVCFs on all of them together or process the samples in two different groups based on their coverage.
And more specifically I would like to know, if different coverage samples mixed on GenotypeGVCF would introduce bias on the results, maybe towards the highest coverage group.