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 resequencing, gVCF is also an appropriate choice to represent and compress results.
gVCF is a text file format, stored as a gzip compressed file (*.genome.vcf.gz). Compression is further 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 like depth and genotype quality reflect the minimum of any site in the block. The gVCF file can be indexed (creating a *.tbi file) and used with existing VCF tools such as tabix and IGV, making it convenient both for direct interpretation and as a starting point for further analysis.
Apps that use gVCF files find it when kicked off and direct it to the sample. If using gVCF files in other tools, download the file to use it in the outside tool.
Each gVCF file contains 1 sample.
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