Options
ImputAccur: fast and user-friendly calculation of genotype-imputation accuracy-measures
Date Issued
2022-08-04
Author(s)
DOI
10.1186/s12859-022-04863-z
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
.
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
.
File(s)
No Thumbnail Available
Name
12859_2022_Article_4863.pdf
Size
1.29 MB
Checksum (MD5)
9b59805e360ea0070cef67cf59de3aef
