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 are provided below. 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.

Version Platform file
v2.2.1*Mac OS X (Apple)qctool_v2.2.1-osx-m1.tgz
v2.2.0*Mac OS X (Intel)qctool_v2.2.0-osx.tgz
v2.2.0*CentOS Linux 7.8qctool_v2.2.0-CentOS_Linux7.8.2003-x86_64.tgz
v2.0.8Mac OS Xqctool_v2.0.8-osx.tgz
v2.0.8CentOS Linux 7.6qctool_v2.0.8-CentOS_Linux7.6.1810-x86_64.tgz
* This is the recommended version; older versions are unsupported but may still appear here for posterity.

Downloading source

The source code to qctool is available as a fossil repository at https://code.enkre.net/qctool. To obtain source code, use the fossil command-line client, or alternatively download a tarball from this table. (Note that this currently generates a tarball on the fly, which may take a while).

* This is the recommended version; only use the development version if you want to try recently implemented features.

Versioning scheme

As of version 2.1, QCTOOL will follow a versioning scheme whereby odd minor numbers (2.1.x etc.) represent development work while even numbers (2.2.x etc.) represent release versions. The current latest release versions are 2.2 version.


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

$ cd qctool
$ ./waf configure
$ ./waf

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

You can check qctool is working by running it:

$ ./build/release/qctool_v<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.