MethylGenotyper Accurate estimation of SNP genotypes from DNA methylation data
Introduction
MethylGenotyper aims to call genotypes from three types of probes in Infinium methylation array: SNPs probes, Type I probes with SNPs at the extension bases causing color-channel-switching, and Type II probes with SNPs at the extension bases. By properly modeling the relationship between methylation intensity and SNP genotypes, MethylGenotyper can produce accurate genotypes for ~4000 SNPs from EPIC array and ~2000 SNPs from 450K array, enables accurate estimation of population structure and genetic relatedness. We have wrapped all these functions into MethylGenotyper and strongly encourage researchers to incorporate it into the EWAS pipeline to maximize statistical power and avoid spurious association signals.
Publications
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Credits
- Chaolong Wang chaolong@hust.edu.cn Investigator
School of Public Health, Huazhong University of Science and Technology, China
- Yi Jiang jiangyi3029@hust.edu.cn Developer
School of Public Health, Huazhong University of Science and Technology, China
Community Ratings
Usability | Efficiency | Reliability | Rated By |
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Accession | BT007466 |
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Tool Type | Application |
Category | DNA methylation |
Platforms | Linux/Unix, MAC, Windows |
Technologies | R |
User Interface | Terminal Command Line |
Latest Release | 1.0 (April 24, 2024) |
Download Count | 302 |
Country/Region | China |
Submitted By | Chaolong Wang |
This study is supported by grants from National Natural Science Foundation of China (82325044, 82021005), the China Postdoctoral Science Foundation (2021M701318), the Natural Science Fund for Distinguished Young Scholars of Hubei Province, China (2022CFA046), and the Fundamental Research Funds for the Central Universities, China (HUST: 2019kfyXJJS036, 2023BR030). Genetic and DNAm data in the AIBL study were funded by the National Health and Medical Research Council in Australia (GNT1161706, GNT1151854).