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

• Published in: BMC bioinformatics Vol. 23; no. 1; pp. 316 - 6
• Main Authors: Thormann, Kolja A., Tozzi, Viola, Starke, Paula, Bickeböller, Heike, Baum, Marcus, Rosenberger, Albert
• Format: Journal Article
• Language: English
• Published: London BioMed Central 04.08.2022; Springer Nature B.V; BMC
• Subjects: Accuracy; Algorithms; Bioinformatics; Biomedical and Life Sciences; Chromosomes; Classification; Computational Biology/Bioinformatics; Computer Appl. in Life Sciences; Data analysis; Filtration; Genome-wide association studies; Genome-Wide Association Study; Genomes; Genotype; Genotype & phenotype; Genotypes; GWAS; Imputation; Life Sciences; Marker selection; Markers; Microarrays; Names; Polymorphism, Single Nucleotide; Quality control; SNP; Software; Source code; Marker selection; Accuracy; Imputation; GWAS; SNP; Quality control
• ISSN: 1471-2105; 1471-2105
• DOI: 10.1186/s12859-022-04863-z

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 .