Genome VCF (gVCF)

Human genome sequencing applications require sequencing information for both variant and nonvariant positions, yet there is no common exchange format for such data. gVCF addresses this issue.

gVCF is a set of conventions applied to the standard variant call format (VCF). These conventions allow representation of genotype, annotation, and additional information across all sites in the genome, in a reasonably compact format. Typical human whole-genome sequencing results expressed in gVCF with annotation are less than 1.7 GB, or about 1/50 the size of the BAM file used for variant calling.

gVCF is also equally appropriate for representing and compressing targeted sequencing results. Compression is achieved by joining contiguous nonvariant regions with similar properties into single ‘block’ VCF records. To maximize the utility of gVCF, especially for high stringency applications, the properties of the compressed blocks are conservative. Block properties such as depth and genotype quality reflect the minimum of any site in the block. The gVCF file is also a valid VCF v4.1 file, and can be indexed and used with existing VCF tools such as tabix and IGV. This feature makes the file convenient both for direct interpretation and as a starting point for further analysis.