Mega2, the Manipulation Environment for Genetic Analysis

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Mega2
Original authorsPrevious Programmers: Charles P. Kollar, Nandita Mukhopadhyay, Lee Almasy, Mark Schroeder, William P. Mulvihill.
DevelopersDaniel E. Weeks, Robert V. Baron, Justin R. Stickel.
Initial release16 January 2000; 26 years ago (2000-01-16)
Stable release
5.0.1 / 13 December 2018; 7 years ago (2018-12-13)
Repository
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Written inC++
Engine
    Lua error in Module:EditAtWikidata at line 29: attempt to index field 'wikibase' (a nil value).
    Operating systemLinux, Mac OS X, Microsoft Windows
    TypeApplied statistical genetics, Bioinformatics
    LicenseGNU General Public License version 3
    Websitewatson.hgen.pitt.edu/register/

    Mega2 is a data manipulation software for applied statistical genetics. Mega is an acronym for Manipulation Environment for Genetic Analysis.

    The software allows the applied statistical geneticist to convert one's data from several input formats to a large number output formats suitable for analysis by commonly used software packages.[1][2][3][4] In a typical human genetics study, the analyst often needs to use a variety of different software programs to analyze the data, and these programs usually require that the data be formatted to their precise input specifications. Conversion of one's data into these multiple different formats can be tedious, time-consuming, and error-prone. Mega2, by providing validated conversion pipelines, can accelerate the analyses while reducing errors.

    Mega2 produces a common intermediate data representation using SQLite3, which enables the data to be accessed by other programs and languages. In particular, the Mega2R R package converts the SQLite3 data into R data frames. Several R functions are provided that illustrate how data can be extracted from the data frames for common R analysis, such as SKAT and pedgene. The key is being able to efficiently extract genotypes corresponding to chosen subsets of markers so as to facilitate gene-based association testing by automating looping over genes in the genome. Another function converts to VCF format and another converts the data to GenABEL format. For more information about the Mega2R package, see here.

    Mega2 has been used to facilitate genetic analyses of a wide variety of human traits, including hereditary dystonia,[5] Ehlers-Danlos syndrome,[6] multiple sclerosis,[7] and gliomas.[8] A list of PubMed Central articles citing Mega2 can be seen here.

    Mega2, which focusses on data reformatting, should not be confused with the MEGA, Molecular Evolutionary Genetics Analysis program, which focuses on molecular evolution and phylogenetics.

    Input file formats

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    Mega2 accepts input data in a variety of widely used file formats. These contain, at a minimum, data about the phenotypes, the marker genotypes, any family structures, and map positions of the markers.

    Input format Description Links
    LINKAGE[9][10][11][12] pre-Makeped or post-Makeped formats Linkage User Guide (PDF), LINKAGE format
    Mega2[1][2][3][4] simplified/augmented LINKAGE-format Mega2 format
    PLINK[13] ped format or binary bed format PLINK documentation
    VCF or BCF[14] Variant Call Format or Binary Variant Call Format Variant Call Format (Wikipedia entry), BCF documentation
    IMPUTE2[15][16] IMPUTE2 GEN and BGEN Formats IMPUTE2 documentation, GEN format, BGEN format

    Output file formats

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    Mega2 supports conversion to the following output formats.

    Output format Links
    ASPEX format ASPEX
    Allegro format[17]
    Beagle format[18][19] BEAGLE
    CRANEFOOT format[20] CRANEFOOT
    Eigenstrat format[21][22] EIGENSOFT
    FBAT format[23] FBAT
    GeneHunter format[24] GeneHunter
    GeneHunter-Plus format[25] GeneHunter-Plus
    IQLS/Idcoefs format[26][27] IQLS,Idcoefs
    Linkage format[9][10][11][12] Linkage User Guide (PDF), LINKAGE format
    Loki format[28] Loki
    MaCH/minimac3 format[29][30] MaCH, minimac3
    MLBQTL format[31] MLB-QTL
    Mega2 annotated format[1][2][3][4] Mega2 format
    Mendel format[32] Mendel
    Merlin format[33] Merlin
    Merlin/SimWalk2-NPL format[33][34] Merlin SimWalk2
    PANGAEA MORGAN format[35][36] MORGAN
    PAP format[37] PAP
    PLINK format[13] (bed, lgen, or ped formats) PLINK
    PREST format[38][39] PREST
    PSEQ format PSEQ
    Pre-makeped LINKAGE format[9][10][11][12] Linkage User Guide (PDF), LINKAGE format
    ROADTRIPS format[40] ROADTRIPS
    SAGE format SAGE, openSAGE
    SHAPEIT format[41][42][43][44][45] SHAPEIT
    SIMULATE format[46] SIMULATE
    SLINK format[47][48] FASTSLINK
    SOLAR format[49][50] SOLAR
    SPLINK format[51] SPLINK
    SUP format[48][52] SUP
    SimWalk2 format[34] SimWalk2
    Structure format[53][54][55] Structure
    VCF format[14] Variant Call Format (Wikipedia entry)
    Vintage Mendel format[32][56] Vintage Mendel
    Vitesse format[57] Vitesse

    Documentation

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    The Mega2 documentation is available here in HTML format, and here in PDF format.

    References

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