Converting from Mega2 format to IQLS/Idcoefs format with Mega2

The free Mega2 software can convert from Mega2 format to IQLS/Idcoefs format, as well as to a number of other formats.

During an association or linkage analysis project, it can often be quite difficult to get one's data in the proper format desired by each different computer program. Not only must the data be transformed to the proper format, but also the loci must be reordered into their proper order. To address this problem, we created Mega2, which can be obtained from our software distribution site. 

Mega2 greatly eases and automates the tedious error-prone process of reformatting one's data from one format to another.

For additional information, please see the Mega2 documentation.

Input: Mega2 format

For further information about Mega2, see:

• Mega2 Input documentation: Mega2
• Mega2 format
• Mukhopadhyay N, Almasy L, Schroeder M, Mulvihill WP, Weeks DE. (1999) Mega2, a data-handling program for facilitating genetic linkage and association analyses. Am J Hum Genet 65
• Mukhopadhyay N, Almasy L, Schroeder M, Mulvihill WP, Weeks DE. (2005) Mega2: data-handling for facilitating genetic linkage and association analyses. Bioinformatics 21(10):2556–2557. doi: 10.1093/bioinformatics/bti364. PMID: 15746282.
• Kollar CP, Baron RV, Mukhopadhyay N, Weeks DE. (October 2013) Mega2: enhanced data-handling for facilitating genetic linkage and association analyses. Presented at the 63rd Annual Meeting of The American Society of Human Genetics, Boston http://abstracts.ashg.org/cgi-bin/2013/ashg13s.pl?author=kollar&sort=ptimes&sbutton=Detail&absno=130121140&sid=32111
• Baron RV, Kollar C, Mukhopadhyay N, Weeks DE. (2014) Mega2: validated data-reformatting for linkage and association analyses. Source Code Biol Med 9(1):26. doi: 10.1186/s13029-014-0026-y. PMID: 25687422. PMC4269913.

Output: IQLS/Idcoefs format

For further information about IQLS/Idcoefs format, see:

• Mega2 Analysis documentation: IQLS/Idcoefs format
• IQLS
• Idcoefs
• Wang Z, McPeek MS. (2009) An Incomplete-Data Quasi-likelihood Approach to Haplotype-Based Genetic Association Studies on Related Individuals. J Am Stat Assoc 104(487):1251–1260. doi: 10.1198/jasa.2009.tm08507.
• Abney M. (2009) A graphical algorithm for fast computation of identity coefficients and generalized kinship coefficients. Bioinformatics 25(12):1561–1563. doi: 10.1093/bioinformatics/btp185.

Mega2 documentation

Documentation for Mega2 is available here in both HTML and PDF format.

Downloading Mega2

Mega2 can be obtained from our software distribution site.

Pre-compiled executables are available for Linux, Macintosh, Solaris, and Windows (native, Cygwin, MinGW).

Citing Mega2

Baron RV, Kollar C, Mukhopadhyay N, Weeks DE
Mega2: validated data-reformatting for linkage and association analyses
Source Code for Biology and Medicine. 2014, 9:26
DOI: 10.1186/s13029-014-0026-y

Baron RV, Kollar CP, Mukhopadhyay N, Almasy L, Schroeder M, Mulvihill WP, Weeks DE (2015) Mega2 (Version 4.9.1). https://watson.hgen.pitt.edu

Support, bug reports, and feedback

 Mega2 Google Group

 Bug reports

• Program Name: Mega2
• Program Version: [Mega2 prints out a version number when you first start it up.]
• Platform: [Windows, Macintosh, Linux, etc.]
• Description:
• Example files: [If you can, please send us example files that will allow us to try to re-create the bug on our own computers.]

  Contact information

Daniel E. Weeks, Ph.D. Professor of Human Genetics and Biostatistics
Department of Human Genetics
Graduate School of Public Health
University of Pittsburgh
Crabtree Hall, Room A303
130 DeSoto Street
Pittsburgh, PA 15261
USA

1 412 624-5388
FAX: 1 412 624-3020
E-mail: weeks@pitt.edu
Web page: https://watson.hgen.pitt.edu

Grant Acknowledgments