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

Area of Science:

• Genetics
• Bioinformatics

Background:

• Genotype imputation is crucial for genome-wide association studies (GWAS) to infer missing genetic variants.
• Ensuring high accuracy of imputed genotypes is fundamental for reliable GWAS results.
• Existing genotype imputation accuracy measures are fragmented across different platforms, posing practical challenges.

Purpose of the Study:

• To introduce ImputAccur, a unified software tool for measuring genotype imputation accuracy.
• To provide a practical solution for assessing imputation quality across various imputation software outputs.

Main Methods:

• ImputAccur processes standard output files from imputation software.
• It derives key accuracy metrics including info, Iam-hiQ, and r²-based indices.
• The tool supports sample/probe and marker filtering.

Main Results:

• ImputAccur enables the derivation of multiple genotype imputation accuracy measures from common imputation software outputs.
• The software facilitates accurate marker filtering prior to downstream data analysis.
• It offers a consolidated approach to assessing imputation quality.

Conclusions:

• ImputAccur provides a practical and unified solution for genotype imputation accuracy assessment.
• The tool enhances the reliability of GWAS by enabling precise marker selection.
• Source code and example data are freely available for use and reproducibility.