Thormann KA, Tozzi V, Starke P, Bickeböller H, Baum M, Rosenberger A. ImputAccur: fast and user-friendly calculation of genotype-imputation accuracy-measures.
BMC Bioinformatics 2022;
23:316. [PMID:
35927623 PMCID:
PMC9351229 DOI:
10.1186/s12859-022-04863-z]
[Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Accepted: 07/27/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND
ImputAccur is a software tool to measure genotype-imputation accuracy. Imputation of untyped markers is a standard approach in genome-wide association studies to close the gap between directly genotyped and other known DNA variants. However, high accuracy for imputed genotypes is fundamental. Several accuracy measures have been proposed, but unfortunately, they are implemented on different platforms, which is impractical.
RESULTS
With ImputAccur, the accuracy measures info, Iam-hiQ and r2-based indices can be derived from standard output files of imputation software. Sample/probe and marker filtering is possible. This allows e.g. accurate marker filtering ahead of data analysis.
CONCLUSIONS
The source code (Python version 3.9.4), a standalone executive file, and example data for ImputAccur are freely available at https://gitlab.gwdg.de/kolja.thormann1/imputationquality.git .
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