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BED/BIM/FAM

Definition
AI-generated

BED/BIM/FAM is the classic PLINK 1 binary genotype trio: `.bed` stores sample-by-variant genotypes in compact binary form, `.bim` stores variant metadata, and `.fam` stores sample metadata.

Topics
Formats
Synonyms
PLINK 1 binary genotype trio
URL
https://www.cog-genomics.org/plink/1.9/formats#bed
Related
BGEN Genotype PGEN

Why it matters in GWAS

Many QC, PCA, relatedness, and association workflows still begin from BED/BIM/FAM because the format is simple and broadly supported. Understanding which information lives in each companion file helps prevent sample-order, allele-label, and coordinate mismatches during conversion to VCF, BGEN, or PGEN.

Example usage

"We converted the cohort VCF to PLINK BED/BIM/FAM before sample QC, PCA, and KING kinship estimation."

BGEN Genotype PGEN PLINK Principal Component Analysis (PCA) 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

  • Purcell S, et al. (2007). PLINK: a tool set for whole-genome association and population-based linkage analyses. Am J Hum Genet.
  • PLINK 1.9 file format reference: https://www.cog-genomics.org/plink/1.9/formats
← Browser Extensible Data (BED) BEDPE →

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