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BGEN

Definition
AI-generated

BGEN is a binary file format (Oxford / UK Biobank style) for storing large-scale genotype or imputed-dosage data compactly, including probabilities or dosages per sample and variant.

Topics
Formats
URL
https://www.cog-genomics.org/plink/2.0/input#oxford
Related
Genotype Dosage Genotype Imputation Genome-Wide Association Study (GWAS)

Why it matters in GWAS

Major biobanks distribute imputed data as BGEN; workflows often convert or analyze BGEN directly with PLINK 2, Hail, or QCTOOL-compatible tools without expanding to full VCF.

Example usage

"Imputed chromosome files in BGEN 1.2 were filtered with PLINK 2 --bgen and merged for association testing."

Genotype Dosage Genotype Imputation Genome-Wide Association Study (GWAS) PLINK UK Biobank
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

  • Band G, Marchini J. (2017). BGEN format. https://www.well.ox.ac.uk/~gav/bgen_format/
  • PLINK 2.0 Oxford / BGEN: https://www.cog-genomics.org/plink/2.0/input#oxford
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