Converting from LINKAGE format to Merlin/SimWalk2-NPL format with Mega2
The free Mega2 software can convert from LINKAGE format to Merlin/SimWalk2-NPL 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: Merlin/SimWalk2-NPL format
For further information about Merlin/SimWalk2-NPL format, see:
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
If you use Mega2 as part of a
published work, please remember to reference Mega2. You may
reference it by citing the following:
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
as well as citing the web site
and the version that you used. For example, the web site citation
for version 4.9.1 should be:
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
If you encounter a bug in Mega2,
please send us a detailed bug report, including the following
information:
- 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.]
Please send your bug reports and
feedback to: Daniel E. Weeks at weeks@pitt.edu
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
Mega2 is currently supported by
the University of Pittsburgh and the following NIH grant:
R01GM076667 (Weeks, Daniel E).
Prior work on Mega2 was partly
supported by R01AG16989 (D.E.W.), R01HG00932 (D.E.W.), and
R01AG16992 (to Jeffrey R. O'Connell).
In addition, parts of Mega2
were inspired by data generated under NIH grant R01DK55406 to
Ranjan Deka.