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
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
For further information about VCF or BCF, see:
For further information about PLINK format, see:
Documentation for Mega2 is available here
in both HTML and PDF format.
Mega2 can be obtained from our software
Pre-compiled executables are available for Linux, Macintosh,
Solaris, and Windows (native, Cygwin, MinGW).
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
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
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: https://watson.hgen.pitt.edu