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Biallelic Variant

Definition
AI-generated

A biallelic variant is a site represented with exactly two alleles in the analysis—typically a reference allele and one alternative allele—so each diploid genotype is a pair drawn from those two states.

Topics
Core genetics
Related
Alternative Allele Genotype Multiallelic Variant

Why it matters in GWAS

Effect sizes, allele frequencies, and meta-analysis harmonization are defined relative to a chosen effect allele; biallelic assumptions simplify QC and software, but splitting or merging multiallelic records incorrectly can distort counts and association tests.

Example usage

"We retained only multiallelic sites split into biallelic variant records for association testing to simplify harmonization across cohorts and software."

Alternative Allele Genotype Multiallelic Variant Reference Allele Single Nucleotide Polymorphism (SNP) Single Nucleotide Variant (SNV) Variant Calling Variant Call Format (VCF)
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References

  • Danecek P, et al. (2021). Twelve years of SAMtools and BCFtools. Gigascience.
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