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Variant normalization

Definition
AI-generated

Variant normalization rewrites variants to a canonical representation—often left alignment and parsimony for indels—so the same haplotype is described consistently across pipelines.

Topics
Sequencing Data Analysis
Related
Indel Multi-allelic variant Variant Call Format (VCF)

Why it matters in GWAS

Without normalization, duplicate records and mismatched alleles break meta-analysis and annotation joins.

Example usage

"Variant normalization with bcftools left-aligned indels before liftover to hg38."

Indel Multi-allelic variant 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

  • Tan A, et al. (2015). Unified representation of genetic variants. Bioinformatics.
← Variant Missingness Variant Quality Score Recalibration (VQSR) →

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