<p>We want use different genomic analysis tools like samtools,bcftool,plink etc</p>

<p>Which operating system should we use?</p>

You can pretty much use any Linux or BSD UNIX you want. Most likely you will get familiar with the [package manager][1] for that platform.

If you use OS X, for instance, you might install [Homebrew][2] and install scientific packages made available via [Homebrew Science][3], which is usually as easy as: `$ brew install homebrew/science/some_package`

For other platforms, like some flavor of Linux, you might use [yum][4] or [rpm][5] (Red Hat/Fedora) or [apt-get][6] (Ubuntu/Debian).

If a package isn't available, you can almost always compile it from source code via GCC under Linux, or Clang/LLVM under OS X (via Xcode).

 [1]: http://en.wikipedia.org/wiki/Package_manager
 [2]: http://brew.sh
 [3]: https://github.com/Homebrew/homebrew-science
 [4]: http://en.wikipedia.org/wiki/Yellowdog_Updater,_Modified
 [5]: http://en.wikipedia.org/wiki/RPM_Package_Manager
 [6]: http://en.wikipedia.org/wiki/Advanced_Packaging_Tool