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Hi, thank you for your forum post. If you need to specify the /source and /target switches sadly you cannot make use of the WHERE clause filter in a command line comparison. However, there is a workaround. If you use the GUI and save the project, you can then use the /project switch in place of the /source and /target switches. If the project file referenced has been configured with a WHERE clause, the clause will be included in the command line comparison.
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I'm using ROWVERSIONs in my tables for change detection and hence I'll want to be able to pass in a filter for something like WHERE Product.RowVersionNumber > @ProductRowVersion. Of course this will change every time I want to run the comparison, but it will dramatically speed up the process.