vcf

VCF stands for Variant Call Format, a text-based file format used to store genetic variation data identified in high-throughput sequencing experiments. It has become the de facto standard for representing variants such as single nucleotide polymorphisms (SNPs), small insertions and deletions (indels), and, with certain conventions, some larger structural variants.

A VCF file begins with a series of metadata lines that start with two hash marks (##), describing the format, the reference genome, and various filters or annotations. The header line that starts with a single hash and the word CHROM defines the column titles for the data rows. The standard columns are CHROM, POS, ID, REF, ALT, QUAL, FILTER, INFO, FORMAT, followed by one or more sample genotype columns. CHROM is the chromosome or contig name, POS is a 1-based coordinate, and REF is the reference allele. ALT holds one or more alternative alleles, separated by commas for multi-allelic sites. QUAL is the Phred-scaled quality score, FILTER indicates whether the variant passed predefined filters, and INFO carries optional key=value fields with additional attributes. FORMAT describes the genotype fields for each sample, and the subsequent sample columns provide per-sample data such as genotype (GT), read depth (DP), and genotype quality (GQ).

VCF files may store multi-allelic variants, phasing information, and annotations. They are frequently compressed with bgzip and indexed with tabix to enable efficient querying. A binary version, BCF, exists for more compact storage. VCF is widely used in variant discovery, population genetics, and downstream analyses with tools such as GATK, bcftools, and vcftools.

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