Skip to content

Genotype likelihood

Definition
AI-generated

Genotype likelihoods are unnormalized probabilities (or log-likelihoods) of genotypes given read data, before hard assignment.

Topics
Sequencing Data Analysis
Related
GenomicsDB Genotype quality (GQ) Joint genotyping

Why it matters in GWAS

Likelihoods feed joint genotyping, imputation from low-coverage sequencing, and probabilistic association models that avoid thresholded hard calls.

Example usage

"Genotype likelihood–based tests in REGENIE used sequencing data without hard-thresholded GT calls."

GenomicsDB Genotype quality (GQ) Joint genotyping Phred-scaled genotype likelihoods (PL) PL and GQ Phred quality score
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

  • McKenna A, et al. (2010). The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data. Genome Res.
← Genotype-level filter Genotype quality (GQ) →

Last updated (UTC · Git history)