ImputAccur: fast and user-friendly calculation of genotype-imputation accuracy-measures

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 fundame...

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Detalles Bibliográficos
Autores principales: Thormann, Kolja A., Tozzi, Viola, Starke, Paula, Bickeböller, Heike, Baum, Marcus, Rosenberger, Albert
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2022
Materias:
Software
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9351229/
https://www.ncbi.nlm.nih.gov/pubmed/35927623
http://dx.doi.org/10.1186/s12859-022-04863-z
Descripción
Sumario: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 r(2)-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. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12859-022-04863-z.

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