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 documentation page for a description 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.

Contact. Please send any questions or reports of issues to the the OXSTATGEN mailing list.

Change history. QCTOOL version 2 is currently in 'release candidate' state. This means some features may not work, or not work well, or work wrongly, or destroy your computer, or your sanity. The best place to receive support is on the OXSTATGEN mailing list. QCTOOL also has a public issue tracker.

QCTOOL v2 also differs in several important ways from the v1 release series. Some important changes in QCTOOL v2 relative to v1 are:

Acknowledgements. The following people contributed to the design and implementation of qctool:

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 wiki.