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 exe

SUBMITTER: Thormann KA 

PROVIDER: S-EPMC9351229 | biostudies-literature | 2022 Aug

REPOSITORIES: biostudies-literature