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PLINK

Whole genome association analysis toolset

Description

PLINK is a free, open-source whole genome association analysis toolset, designed to perform a range of basic, large-scale analyses in a computationally efficient manner.

The focus of PLINK is purely on analysis of genotype/phenotype data, so there is no support for steps prior to this (e.g. study design and planning, generating genotype or CNV calls from raw data). Through integration with gPLINK and Haploview, there is some support for the subsequent visualization, annotation and storage of results.

PLINK (one syllable) is being developed by Shaun Purcell at the Center for Human Genetic Research (CHGR), Massachusetts General Hospital (MGH), and the Broad Institute of Harvard & MIT, with the support of others.

For more details, visit the PLINK website

The latest stable source release of PLINK (1.07) has been modified by our research group, In Silico. All of the modifications are licensed GPLv2, same as PLINK. Our changes, also highlighted in the ChangeLog file, are:

  • Addition of a complete Autotools build system (./configure && make && make install)
  • Creation of PLINK library (libplink) that exposes functionality that may be imported by third-party software
  • OpenMP support in epistasis calculation
  • Numeric attribute support (currently only available in library)
  • zlib is now a required library

Dependencies

  • The libz/zlib compression library is required, but this is installed by default on most Unix systems. In MinGW libz is installed via mingw-get.

  • LAPACK is a soft dependency: not explicitly required, but highly encouraged to take advantage of linear algebra routines that have decades of optimization.

  • Finally, OpenMP is required to take advantage of the parallelized epistasis analysis code. This is another library typically installed alongside the compiler toolchain.

Compilation Environment and Instructions

To compile this code, a GNU toolchain and suitable environment are required. GNU g++ has been used to successfully compile the code.

We have successfully built and run PLINK on:

  • Linux (64-bit Ubuntu) (gcc-4.6)
  • Mac (10.6 - 10.7) (gcc-4.2.1)
  • Windows 7 (32-bit) using the MinGW compiler system (gcc-4.6)

To build PLINK, first run the bootstrap script

./bootstrap.sh

This calls autoreconf and generates the configure script. From this point, a standard

./configure && make && sudo make install

will generate the Makefile, compile and link the code, and copy the objects to the installation directory (default of /usr/local). As is convention, headers are installed in $PREFIX/include, binary in $PREFIX/bin, and the library in $PREFIX/lib.

The PLINK library (libplink) can be used to use PLINK functionality in third-party code. See our Encore project for a good example of this.

The resulting binary plink/plink.exe will run with the same command-line options as the official binary version of PLINK that can be downloaded from the website.

Contributors

See AUTHORS file.

References

Purcell S, Neale B, Todd-Brown K, Thomas L, Ferreira MAR, Bender D, Maller J, Sklar P, de Bakker PIW, Daly MJ & Sham PC (2007) PLINK: a toolset for whole-genome association and population-based linkage analysis. American Journal of Human Genetics, 81.