How can I change the affected/unaffected status of a sample to run new algorithmic filters?

In order to run algorithmic filters for segregating variants, you need to set which is the affected and unaffected sample respectively. You can do that by selecting, from the "Analysis Actions" button on the top right corner of the merged analysis you can see in the Dashboard page, the "Update samples affected status" option.

You will be directed to a screen, as the one shown below:

You can delete the filters displayed, then update the affected/unaffected status of your samples and run the algorithmic filters you would like for your merged analysis.