QCTOOL is a command-line utility program for manipulation and quality control of gwas datasets and other genome-wide data. QCTOOL can be used
- To compute per-variant and per-sample QC metrics.
- To filter out samples or variants.
- To merge datasets in various ways.
- To convert dataset between file formats. (In particular QCTOOL can read and write BGEN files, including full support for the BGEN v1.2 format that has been used for the UK Biobank imputed data full release).
- To manipulate datasets in various ways - e.g. by updating data fields or aligning alleles to a reference sequence based on information in a strand file.
- To annotate variants with information from BED files, sequence from FASTA files, or with genetic map positions.
- To compute LD metrics between variants.
- To compare genotypes for individuals typed or imputed or phased in different datasets.
- To compute between-sample relatedness and principal components.
- To compute 'genetic risk predictor' scores.
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.
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.
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.
For more information or questions, please contact the OXSTATGEN mailing list at
oxstatgen (at) jiscmail.ac.uk