Genome VCF Files
Genome VCF (gVCF) files are VCF v4.1 files that follow a set of conventions for representing all sites within the genome in a reasonably compact format. The gVCF files include all sites within the region of interest in a single file for each sample.
The gVCF file shows no-calls at positions with low coverage or where a low-frequency variant (< 3%) occurs often enough (> 1%) that the position cannot be called to the reference. A genotype (GT) tag of ./. indicates a no-call.
If the genotypes of interest feature is on, the gVCF file can have additional rows showing the variant calls of interest as requested by the user. These calls can have a filter value of ForcedReport, indicating the calls are forced to be written to the gVCF file.
For more information, see sites.google.com/site/gvcftools/home/about-gvcf.