VCF — Variant Call Format

Overview

VCF is the standard format for storing genomic variant data, including single nucleotide polymorphisms, insertions and deletions, structural variants, and copy number variants. Developed by the 1000 Genomes Project in 2010 and now maintained by GA4GH through the hts-specs community, VCF is the output format of variant calling pipelines and the input to downstream association and functional annotation analyses. BCF (Binary Call Format) is the compressed binary equivalent for efficient storage and access. VRS (Variant Representation Specification) is a computationally precise complement to VCF, providing globally unique content-addressed identifiers for variants that resolve ambiguities arising from differing genome builds and HGVS notations.

Connections

• Governed by: GA4GH (hts-specs)
• Companion format: SAM-BAM-CRAM (aligned reads from which variants are called)
• Complement: VRS (computationally precise variant identifiers)

Resources

• https://samtools.github.io/hts-specs/VCFv4.4.pdf (VCF 4.4 specification)
• https://github.com/samtools/hts-specs