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Genotype quality (GQ)

Definition
AI-generated

Genotype quality (GQ) is a Phred-scaled estimate of error for the called genotype at a site, typically derived from genotype likelihoods in the VCF FORMAT field.

Topics
Sequencing Data Analysis
Related
Genotype likelihood Genotype-level filter GenomicsDB

Why it matters in GWAS

GQ thresholds control missingness and false heterozygotes in sequencing-based association; they interact with depth and allele balance filters.

Example usage

"We removed genotypes with GQ < 20 before burden aggregation."

Genotype likelihood Genotype-level filter GenomicsDB No-call Phred-scaled genotype likelihoods (PL) PL and GQ
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

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