v1.2.1
Improved handling of DeepVariant non-called gVCF records
Compared to other callers, DeepVariant generates more non-called (GT=./.) gVCF records to represent uncertainty in poorly-covered or ambiguous sites; including both reference bands and variant records. Earlier versions of GLnexus omitted all QC values in the pVCF entries corresponding to such records. This patch preserves the QC values and introduces a new "Reason for No Call" code, I for Input non-called, to indicate the site or reference band was non-called in the gVCF input.