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GenomicsDB

Definition
AI-generated

GenomicsDB is a columnar storage format and library used to hold many sample gVCFs (or equivalent chunked variant data) for scalable joint genotyping.

Topics
Sequencing Data Analysis Bioinformatics
URL
https://gatk.broadinstitute.org/hc/en-us/articles/360036883491-GenomicsDBImport
Related
Genomic Variant Call Format (gVCF) Genome Analysis Toolkit (GATK) HaplotypeCaller

Why it matters in GWAS

Large WGS studies that report GATK-style joint calling often cite GenomicsDB as the backing store for thousands of samples; recognizing it clarifies how cohort call sets are assembled and why disk layout and import intervals matter for reproducibility.

Example usage

"gVCFs were consolidated with GenomicsDBImport into a GenomicsDB store per chromosome, then jointly genotyped with GenotypeGVCFs."

Genomic Variant Call Format (gVCF) Genome Analysis Toolkit (GATK) HaplotypeCaller Joint genotyping Variant Call Format (VCF)
Related-term network

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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

  • Poplin R, et al. (2018). Scaling accurate genetic variant discovery to tens of thousands of samples. Nature. https://doi.org/10.1038/nature24239
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