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Input and output support for the widely-used PLINK format files.

Input and output support for Mega2 format files that contain informative header lines and are readable into R. The ability to align allele labels to a reference and to resolve strand issues.

The availability of our Genetic Map Interpolator for aiding in constructing genetic maps of markers. The ability to run in an automated way using batch files. The ability to create custom tracks of results for visualization in the UCSC genome browser. The ability to create publication-quality PDF plots of the results using our nplplot library. In addition to the ability to reformat data for a variety of analysis programs, other useful features of Mega2 include: Mega2 can also be run in a hands-free mode, using a control or ‘batch’ file to specify these choices. After the desired output files are created, Mega2 exits. Mega2 is currently structured so that the user proceeds through a series of menus, both to create the database and later to process it, making choices in each menu (or accepting the default values), until the desired output files are created. In addition, for many of these options, it also sets up a shell script that then can automatically run these analyses (if you are using Mega2 in a Unix or Macintosh environment). Mega2 then takes the database file and, via a menu-driven interface, transforms it into various other file formats, thus greatly facilitating a variety of different analyses. The input data are read and validated once, then stored in a ‘SQLite’ database file. For example, trait locus penetrance information can be specified. Mega2 allows one to augment these input formats with additional information, if desired. Mega2 can read input data in several formats: LINKAGE format, PLINK format, IMPUTE format and VCF format. To address these problems, we created Mega2.

Writing custom reformatting scripts can be error-prone and very time-consuming. Not only must the data be converted to the proper format, but also the loci must be reordered into their proper order. Unfortunately, it can often be quite difficult to get one’s data in the proper format desired by each different computer program.

For more information, please see the Mega2 documentation, which is available here: ĭuring an association or linkage analysis project, one may need to analyze the data with several different programs. Here we give a quick overview of the Mega2 C++ program. The Mega2R package uses as input genetic data that have been reformatted and stored in a ‘SQLite’ database this database is initially created by the standalone Mega2 C++ program.