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

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 .

Keywords: Accuracy; GWAS; Imputation; Marker selection; Quality control; SNP.

Fig. 1

Example of real-data genotype-imputation accuracy-measures for the telomere region on chromosome 9. Top left: hiQ, top right: info, centre left: Iam_chance, centre right: Iam_HWE, bottom left: ${\text{r}}_{\text{Beagle}}^2$, bottom right: ${\text{r}}_{\text{MACH}}^2$; each dot represents one imputed marker; the marker size is according to minor allele frequency (MAF); threshold values are freely selectable; vertical lines: centre of region classified as: “cold”, “tepid”, “hot”, or “very hot” (the definition is given in the Additional file 1).