qctool v2
A tool for quality control and analysis of gwas datasets.

Obtaining QCTOOL

QCTOOL is available either as binaries or as source code. The recommended approach is to download and compile the QCTOOL source code on the machine(s) you will be working on. However, for convenience a small number of precompiled binary packages can be found here. These provided as-is and will not work on all platforms; if a suitable version is not available please download the QCTOOL source code and compile instead.

Downloading source

The source code to qctool is available as a mercurial repository hosted on bitbucket. To obtain source code, use the mercurial command-line client hg, a GUI client such as SourceTree, or alternatively download a tarball from the Downloads page on bitbucket.

Please note QCTOOL v2 is currently in 'release candidate' status, please make sure you download code for the beta branch. For example, using the hg command-line tool, the command

$ hg clone -r beta https://gavinband@bitbucket.org/gavinband/qctool

will download source code for the latest beta branch and place it in a newly created qctool directory.


Having downloaded the source code (and extracted it if necessary), a basic compilation sequence would then be:

$ cd qctool
$ ./waf-1.5.18 configure
$ ./waf-1.5.18

If all is successful, this produces an executable ./build/release/qctool_v2.0-<version>

You can check qctool is working by running it:

$ ./build/release/qctool_v2.0-<version> -help

which should print out a list of options.

Further information

The QCTOOL wiki contains further information which may be useful if you are unable to compile QCTOOL or need to tweak compilation for specific platforms.