MagicalRsq-X: A cross-cohort transferable genotype imputation quality metric.

doi:10.1016/j.ajhg.2024.04.001

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MagicalRsq-X: A cross-cohort transferable genotype imputation quality metric.

American journal of human genetics - 2 May 2024

Sun Quan, Yang Yingxi, Rosen Jonathan D, Chen Jiawen, Li Xihao, Guan Wyliena, Jiang Min-Zhi, Wen Jia, Pace Rhonda G, Blackman Scott M, Bamshad Michael J, Gibson Ronald L, Cutting Garry R, O'Neal Wanda K, Knowles Michael R, Kooperberg Charles, Reiner Alexander P, Raffield Laura M, Carson April P, Rich Stephen S, Rotter Jerome I, Loos Ruth J F, Kenny Eimear, Jaeger Byron C, Min Yuan-I, Fuchsberger Christian, Li Yun

Abstract excerpt

Since genotype imputation was introduced, researchers have been relying on the estimated imputation quality from imputation software to perform post-imputation quality control (QC). However, this quality estimate (denoted as Rsq) performs less well for lower-frequency variants. We recently published MagicalRsq, a machine-learning-based imputation quality calibration, which leverages additional typed markers from...

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Identifiers

PMID: 38636510
DOI: 10.1016/j.ajhg.2024.04.001
PMCID: PMC11080605

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PubMed metadata and Literature Corpus relationships. Corpus snapshot updated 7 Sept 2026. Manifest publication-graph-cohort-2026-09-07.1.

Source receipt: pubmed, retrieved 7 Sept 2026.

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