Converting from VCF or BCF format to PLINK format with Mega2

The free Mega2 software can convert from VCF or BCF format to PLINK 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: VCF or BCF format

For further information about VCF or BCF, see:

Output: PLINK format

For further information about PLINK 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).

Support, bug reports, and feedback

 Mega2 Google Group

Mega2 users are invited to participate in our Mega2 Google Group at!forum/mega2-users. Support questions should be posted there.

 Bug reports

If you encounter a bug in Mega2, please send us a detailed bug report, including the following information:
Please send your bug reports and feedback to: Daniel E. Weeks at

  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

1 412 624-5388
FAX: 1 412 624-3020
Web page:

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.