GATK recalibration problems: low coverage and few SNVs

We’ve had reports about very strange results mostly on viral genomes. In such cases very few SNVs will be reported, with odd frequencies and very low coverage. We could trace this back to GATK’s base call recalibration step, in which for yet unknown reasons, most base call qualities are set to the lowest possible value by GATK. We are investigating this and ask users to run LoFreq on the uncalibrated data in such cases (keeping in mind that spurious SNV calls are possible).