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Variant Call Format (VCF)

Definition
AI-generated

VCF is a text-based standard for representing genetic variants, their alleles, site-level metadata, and per-sample genotype fields.

Topics
Formats
URL
https://samtools.github.io/hts-specs/VCFv4.3.pdf
Related
Alternative Allele BGEN Genome Coordinate System

Why it matters in GWAS

VCF is a common interchange format for sequencing, array, and imputation pipelines, so many GWAS workflows begin with VCF and convert onward to PLINK, BGEN, or PGEN. Correct handling of reference allele, coordinate convention, multiallelic sites, and genotype representation is essential for harmonization and reproducibility.

Example usage

"We normalized and indexed the cohort VCF before conversion to PLINK and imputation against the reference panel."

Alternative Allele BGEN Genome Coordinate System Genotype Genotype Dosage Genotype quality (GQ) GenomicsDB PGEN Phred-scaled genotype likelihoods (PL) PL and GQ Reference Allele Variant Calling
Related-term network

Click any node to open that term page.

Node order. The current term is first. Next come every page linked from Related terms, in the same top-to-bottom order as that list. Then new terms appear in two-hop layers: for each of those direct neighbors (in that same order), their related terms are appended if not already listed. A third pass does the same for two-hop nodes. The walk stops when a fixed maximum number of nodes is reached.

References

  • Danecek P, et al. (2011). The variant call format and VCFtools. Bioinformatics. https://doi.org/10.1093/bioinformatics/btr330
  • HTS specifications: https://samtools.github.io/hts-specs/
  • GWASTutorial: Data formats.
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