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

Basic examples

This and the other pages in the 'examples' menu show some basic command lines used to carry out common tasks with QCTOOL. For more information see also the list of options and the diagram 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
Get some summary information about a genotypes file
$ qctool -g <genotypes file>