QCTOOL 2.0-rc8

QCTOOL is a command-line utility program for basic quality control of gwas datasets. It supports the same file formats used by the WTCCC studies, as well as the binary file format described here and the Variant Call Format, and is designed to work seamlessly with SNPTEST and related tools. A typical use of QCTOOL is to compute per-sample and per-SNP summary statistics for a cohort, and use these to filter out samples and SNPs (either by removing them from the files or by writing exclusion lists). QCTOOL can also be used to perform various subsetting and merging operations, and to manipulate sample information in preparation for association testing - as shown on the examples page.

Accessing the software

To load the module:

$ module load QCTOOL/v2.0-rc8-iomkl-2018a

An example command to include in your job script:

$ qctool -g <genotype file>

Accessing Previous Versions

Wherever possible, previous versions of this application will be retained for continuity, especially for research projects that require a consistent version of the software throughout the project. Such versions, however, may be unsupported by IT Services or the applications vendor, and may be withdrawn at short or no notice if they can no longer run on the cluster - for example, essential operating system upgrades may be incompatible with old versions.

Previous versions are available on this service:

Known Problems & Limitations


Other Information

The Support Level for this application is An.

Visit the QCTOOL website for more information regarding this application.

Last modified: 8th June 2018