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.
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