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

Basic examples

This page shows command lines used to carry out common tasks with QCTOOL. We assume the program is being run from a directory containing a sample file example.sample and 22 GEN files named example_01.gen, example_02.gen, etc. As one of the first examples, we convert these files to BGEN format and use this in subsequent examples. See also the list of options.
Run qctool
$ qctool
View the program usage page
$ qctool -help | less
Get a computer-readable list of options
$ qctool -spec
Note: output is is JSON format. This option is used to construct the table of options.
Capture screen output in log file
$ qctool [other options] -log log.txt