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Genomic Variant Call Format (gVCF)

Definition
AI-generated

gVCF is an extension of VCF that reports both variant sites and non-variant reference-confidence blocks, allowing per-sample uncertainty to be retained for joint genotyping.

Topics
Bioinformatics Formats
URL
https://gatk.broadinstitute.org/hc/en-us/articles/360035531692-VCF-Variant-Call-Format
Related
Variant Call Format (VCF) Variant Calling Genotype Calling

Why it matters in GWAS

Jointly genotyped cohorts often start from sample-level gVCF inputs; understanding this format helps interpret callability, missingness, and confidence differences that can affect association results.

Example usage

"The methods explicitly include Genomic Variant Call Format (gVCF) in the end-to-end analysis workflow."

Variant Call Format (VCF) Variant Calling Genotype 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

  • DePristo MA, et al. (2011). A framework for variation discovery and genotyping using next-generation DNA sequencing data. Nature Genetics. https://doi.org/10.1038/ng.806
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