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


QCTOOL is a command-line utility program for manipulation and quality control of gwas datasets and other genome-wide data. QCTOOL can be used

QCTOOL is designed to be as easy-to-use as possible and we hope you find it so. See the basic usage page for a quick start on running QCTOOL, and the diagram of options for an overview of how QCTOOL works.

IMPORTANT: this page documents QCTOOL version 2, which differs in several important ways from the original QCTOOL v1. Version 1 is still available but is now unsupported.

Obtaining QCTOOL

The QCTOOL source code is currently hosted at code.enkre.net. You may also be able to obtain precompiled binaries from this folder. See the download page for full details on obtaining and installing QCTOOL.

Change history

See the change history page.


The following people contributed to the design and implementation of qctool: * Gavin Band * Jonathan Marchini

In addition, QCTOOL contains the SNP-HWE code by Jan Wigginton et al., described in "A Note on Exact Tests of Hardy-Weinberg Equilibrium", Wigginton et al, Am. J. Hum. Genet (2005) 76:887-93. Further acknowledgements can be found on the QCTOOL repository main page.

Getting support

For more information or questions, please contact the OXSTATGEN mailing list at oxstatgen (at) jiscmail.ac.uk