I installed QGIS with Microsoft SCCM 2012 and I want to make a silent install without desktop shortcuts.
I managed to do a silent install with / S but I found no s command to delete desktop shortcuts.
I have Windows 7 64 client PCs
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Although i believe that your question is rather a windows issue (how can i create/change desktop shortcuts), maybe until you solved that problem you can use a portable version of QGIS for your users. Under the following link you can download a full functional QGIS 1.8 version. It already comes with all mayor features and some plugins installed. Extract it to a folder of your choice, add the folder location to the qgis.bat (in case it isn't starting) and execute it to start QGIS.