Why do I see the term UNDEFINED in the VC object?
The VCF files generated by variant callers such as GATK and MuTect are the input files used for variant analysis by the Singular Analysis Toolset. In each VCF file, there are eight fixed fields including an INFO field, which varies widely in composition.
The Singular Analysis Toolset reports the recognizable information to the VC object from the VCF file and also uses the variant group information. If information is unavailable in the VCF file, it will be reported as UNDEFINED in the VC object.