gVCF Files

This application also produces the Genome Variant Call Format file (gVCF). gVCF was developed to store sequencing information for both variant and nonvariant positions, which is required for human clinical applications. gVCF is a set of conventions applied to the standard variant call format (VCF) 4.1 as documented by the 1000 Genomes Project. These conventions allow representation of genotype, annotation, and other information across all sites in the genome in a compact format. Typical human whole-genome sequencing results expressed in gVCF with annotation are less than 1 Gbyte, or about 1/100 the size of the BAM file used for variant calling. If you are performing targeted sequencing, gVCF is also an appropriate choice to represent and compress the results.

gVCF is a text file format, stored as a gzip compressed file (*.genome.vcf.gz). Amplicon gVCF files are not block compressed (one row per reference position).

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