qctool - README

Copyright 2009-2020 Gavin Band, University of Oxford

This package comprises the QCTOOL program for quality control of a set of SNP marker data, together with some other utility programs.

The programs included are

• QCTOOL, a program for manipulation and quality control of gwas datasets and other genome-wide data. Read the QCTOOL documentation.
• Inthinnerator, a program for thinning genetic variants using a recombination map. Read the inthinnerator documentation.

Obtaining QCTOOL

Basic instructions for obtaining and/or compiling QCTOOL can be found on the QCTOOL download page. For further information, see the wiki page on compiling QCTOOL.

Acknowledgements

QCTOOL was written by Gavin Band, based on an initial design by Gavin Band and Jonathan Marchini.

QCTOOL gratefully makes use of functionality from the following projects:

• zlib (http://zlib.net/)
• the boost C++ libraries (http://www.boost.org)
• sqlite3 (http://www.sqlite.org),
• the Eigen library (http://eigen.tuxfamily.org)
• the SNPHWE code from Wigginton et al (http://www.sph.umich.edu/csg/abecasis/Exact)
• the Zstandard library(http://www.zstd.net).