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Variant Quality Score Recalibration (VQSR)

Definition
AI-generated

Variant Quality Score Recalibration (VQSR) trains a model on truth-sensitivity and known sites to assign calibrated VQSLOD scores, replacing fixed hard thresholds for some filters.

Topics
Sequencing Data Analysis
Related
Base Quality Score Recalibration (BQSR) Hard filtering Variant Calling

Why it matters in GWAS

VQSR helps large WGS cohorts retain sensitivity while controlling false positives; it complements rather than replaces explicit hard filters in many pipelines.

Example usage

"SNPs were recalibrated with VQSR using Omni and 1000G training sets."

Base Quality Score Recalibration (BQSR) Hard filtering Variant Calling
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

  • DePristo MA, et al. (2011). A framework for variation discovery and genotyping using next-generation DNA sequencing data. Nat Genet.
← Variant normalization Variation graph →

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