Converting from LINKAGE format to SLINK format with Mega2

The free Mega2 software can convert from LINKAGE format to SLINK 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: LINKAGE format

For further information about LINKAGE, see:

• Mega2 Input documentation: LINKAGE
• Linkage User Guide (PDF)
• LINKAGE format
• Lathrop GM, Lalouel JM. (1984) Easy calculations of lod scores and genetic risks on small computers. Am J Hum Genet 36:460–465.
• Lathrop GM, Lalouel JM, Julier C, Ott J. (1985) Multilocus linkage analysis in humans: detection of linkage and estimation of recombination. Am J Hum Genet 37(3):482–498.
• Lathrop GM, Lalouel JM, White RL. (1986) Construction of human linkage maps: likelihood calculations for multilocus analysis. Genet Epidemiol 3:39–52. doi: 10.1002/gepi.1370030105.
• Lathrop GM, Lalouel JM. (1988) Efficient computations in multilocus linkage analysis. Am J Hum Genet 42:498–505.

Output: SLINK format

For further information about SLINK format, see:

• Mega2 Analysis documentation: SLINK format
• FASTSLINK
• Weeks DE, Ott J, Lathrop GM. (1990) SLINK: a general simulation program for linkage analysis. Am J Hum Genet 47(3):A204.
• Schäffer AA, Lemire M, Ott J, Lathrop GM, Weeks DE. (2011) Coordinated conditional simulation with SLINK and SUP of many markers linked or associated to a trait in large pedigrees. Hum Hered 71(2):126–134. doi: 10.1159/000324177. PMID: 21734403. PMC3136384.

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