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[nickmachnik]

Hey, please have a look at the online documentation, specifically here, the type of analysis you want to conduct is described with an example there. Hope that helps! Best, Nick

[nickmachnik]

For that, you simply don't set the --chromosome flag. That will give you windows for the whole genome. Window and Step are set with the respective positional arguments, as described in the example and in the command line help.

[nickmachnik]

If you are asking what good values for window and step would be: that really depends on what you are looking for. For the window, I would in general say that it is advisable to run the analysis with a number of window sizes to catch different kinds of possible changes, but a good point to start may be 3 mb, as in the example.

step should be greater or equal to the bin size of your data. If you want to scan the whole genome, it should also not exceed half the window size. Within that range it really depends on your computational resources; the smaller the step, the more comparisons will be made, which increases the resolution of your scan. If your computational resources allow, you could start with a step of 100 kb, as in the example.

[nickmachnik]

Moved to a new issue thread. Will close, as the window size question seems answered.