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Mega2: validated data-reformatting for linkage and association analyses.

Baron, Robert V and Kollar, Charles and Mukhopadhyay, Nandita and Weeks, Daniel E (2014) Mega2: validated data-reformatting for linkage and association analyses. Source Code Biol Med, 9 (1). 26 - ?. ISSN 1751-0473

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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


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Item Type: Article
Status: Published
CreatorsEmailPitt UsernameORCID
Baron, Robert Vrvb5@pitt.eduRVB5
Kollar, Charles
Mukhopadhyay, Nanditanandita@pitt.eduNANDITA
Weeks, Daniel Eweeks@pitt.eduWEEKS0000-0001-9410-7228
Date: 14 November 2014
Date Type: Acceptance
Journal or Publication Title: Source Code Biol Med
Volume: 9
Number: 1
Page Range: 26 - ?
DOI or Unique Handle: 10.1186/s13029-014-0026-y
Schools and Programs: School of Public Health > Biostatistics
School of Public Health > Human Genetics
School of Dental Medicine > Dental Science
Refereed: Yes
Uncontrolled Keywords: Association, Data management, Human Genetics, Linkage, Software
ISSN: 1751-0473
Funders: NIGMS NIH HHS (R01 GM076667)
Date Deposited: 22 Dec 2016 14:59
Last Modified: 01 Nov 2017 14:04


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