N. Mukhopadhyay1, L. Almasy1, M. Schroeder2, W.P.
Mulvihill3, D.E. Weeks1.
1) Human Genetics, University of Pittsburgh,
Pittsburgh, PA; 2) Stanford University, Stanford, CA; 3) Carleton College,
Northfield, MN.
During a linkage analysis project, it can be quite difficult to get one's data in the proper format required by each different computer program. Not only must the data be converted to the proper format, but also the loci must be reordered into their proper order. To address this problem, we created Mega2.
A typical linkage-analysis study requires information regarding pedigree structure, trait phenotypes, and genetic marker data. One commonly-used data format is the one used by the LINKAGE programs. LINKAGE-format files come in pairs: the "datain.dat" contains the locus information (disease model, allele frequencies, numbers of alleles, etc.), while the "pedin.dat" contains the pedigree structure information and phenotypes. However, the original LINKAGE format made no provisions for locus names nor for marker map information. So Mega2 uses as input a trio of files which remedy these omissions: 1) the locus file modified to contain locus name information; 2) the pedigree file; and 3) the map file. Mega2 then takes this trio of input files and, via a menu-driven interface, transforms them into various other file formats, thus greatly facilitating a variety of different analyses. In addition, for many of these options, it also sets up a C-shell script that can then automatically run these analyses. Programs that are currently supported include SIMWALK2, MENDEL, ASPEX, APM, SLINK, SPLINK, SIMULATE, SAGE, GeneHunter, GeneHunter-Plus, TDTMax, SOLAR, and Guo and Thompson's program for testing for Hardy-Weinberg equilibrium. In addition, Mega2 can generate summaries about pedigree structures and allele frequencies, as well as can convert larger pedigrees to their component nuclear families.
Mega2 currently uses a textual interface. We plan to use it as the engine behind some more graphical interfaces under development. Mega2 is available via our web site http://watson.hgen.pitt.edu/.
This work was supported in part by the following NIH grants: HG00932, AG16989, AG16992, EY09859, and DK55406.