VCFformat

VCF format, short for Variant Call Format, is a text-based standard used to store genetic variation data and related metadata produced by sequencing experiments and variant calling pipelines. It is widely adopted in genomics for representing single nucleotide variants, small insertions and deletions, and, with limitations, larger structural variants. A VCF file typically exists as a header followed by rows of variant records, enabling easy parsing, filtering, and integration with annotation tools.

The file structure consists of a header section and a data section. Header lines begin with two hash symbols (##) and contain meta-information about the data fields, formats, and filters. The main column header line begins with a single hash (#) and lists the standard columns: CHROM, POS, ID, REF, ALT, QUAL, FILTER, INFO, and optionally FORMAT plus one column per sample. Each data line represents a genomic position where there is a variant, with CHROM indicating the chromosome, POS the 1-based position, and REF/ALT describing the reference and observed alleles, respectively. QUAL provides a quality score, FILTER indicates pass/fail status, and INFO stores semicolon-delimited key=value annotations. When present, FORMAT describes per-sample genotype fields (e.g., GT, DP, GQ), followed by one column per sample.

VCF has several versions, with 4.0, 4.1, and 4.2 being common. It is often compressed using bgzip and indexed with tabix to enable rapid access. The format is supported by many tools (e.g., bcftools, vcftools) and serves as a standard input for downstream annotation and analysis, although it can be large and complex for structural variants.