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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.
For more information, see sites.google.com/site/gvcftools/home/about-gvcf.