Mega2: validated data-reformatting for linkage and association analyses

Source Code for Biology and Medicine

Daniel E Weeks³  Nandita Mukhopadhyay¹  Charles Kollar²  Robert V Baron² 

[1] Department of Oral Biology, School of Dental Medicine, University of Pittsburgh, Pittsburgh 15261, PA, USA;Department of Human Genetics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh 15261, PA, USA;Department of Biostatistics, Graduate School of Public Health, University of Pittsburgh, Pittsburgh 15261, PA, USA

关键词: Data management;    Human Genetics;    Association;    Linkage;    Software;   

Others  :  1139271
DOI  :  10.1186/s13029-014-0026-y

 received in 2014-07-18, accepted in 2014-11-14,  发布年份 2014

【 摘 要 】

Background

In a typical study of the genetics of a complex human disease, many different analysis programs are used, to test for linkage and association. This requires extensive and careful data reformatting, as many of these analysis programs use differing input formats. Writing scripts to facilitate this can be tedious, time-consuming, and error-prone. To address these issues, the open source Mega2 data reformatting program provides validated and tested data conversions from several commonly-used input formats to many output formats.

Results

Mega2, the Manipulation Environment for Genetic Analysis, facilitates the creation of analysis-ready datasets from data gathered as part of a genetic study. It transparently allows users to process genetic data for family-based or case/control studies accurately and efficiently. In addition to data validation checks, Mega2 provides analysis setup capabilities for a broad choice of commonly-used genetic analysis programs. First released in 2000, Mega2 has recently been significantly improved in a number of ways. We have rewritten it in C++ and have reduced its memory requirements. Mega2 now can read input files in LINKAGE, PLINK, and VCF/BCF formats, as well as its own specialized annotated format. It supports conversion to many commonly-used formats including SOLAR, PLINK, Merlin, Mendel, SimWalk2, Cranefoot, IQLS, FBAT, MORGAN, BEAGLE, Eigenstrat, Structure, and PLINK/SEQ. When controlled by a batch file, Mega2 can be used non-interactively in data reformatting pipelines. Support for genetic data from several other species besides humans has been added.

Conclusions

By providing tested and validated data reformatting, Mega2 facilitates more accurate and extensive analyses of genetic data, avoiding the need to write, debug, and maintain one’s own custom data reformatting scripts.

Mega2 is freely available at https://watson.hgen.pitt.edu/register/ webcite.

【 授权许可】

   
2014 Baron et al.; licensee BioMed Central Ltd.

【 图 表 】

Figure 1.

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