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PGEN

Definition
AI-generated

PGEN is the primary binary genotype format used by PLINK 2, accompanied by `.pvar` for variant metadata and `.psam` for sample metadata.

Topics
Formats
URL
https://www.cog-genomics.org/plink/2.0/formats#pgen
Related
BED/BIM/FAM BGEN Genotype Dosage

Why it matters in GWAS

Many current array and imputed-data pipelines use PGEN because it supports large sample sizes and dosage-aware analysis without forcing everything into text-based VCF. Recognizing the companion files and their roles makes conversion, QC, and downstream association testing less error-prone.

Example usage

"Imputed dosages were imported to PGEN and analyzed with plink2 --glm after sample and variant QC."

BED/BIM/FAM BGEN Genotype Dosage PLINK Quality Control (QC) Variant Call Format (VCF)
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

  • Chang CC, et al. (2015). Second-generation PLINK: rising to the challenge of larger and richer datasets. Gigascience. https://doi.org/10.1186/s13742-015-0047-8
  • PLINK 2 file format reference: https://www.cog-genomics.org/plink/2.0/formats#pgen
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