A situation may arise with the preliminary layout where the well/substrate contacts are not added. You may have 4-pin MOS devices in the source but 3-pin MOS devices in the layout temporarily so you want to modify the LVS runset so that the bulk terminal is excluded from LVS. Calibre provides the following command to discard those extra pins:
LVS Discard Pins By Device YES
You can direct LVS to discard extra pins from recognized devices during circuit comparison.
Using the DEVICE statements in your rule file and the instances from both the layout and source, LVS takes into consideration the component type, component subtype, numbers of pins, as well as pin names in the instance to determine if pins can be discarded during comparison.
The Standard Verification Rules Format (SVRF) Manual has multiple examples of using LVS Discard Pins By Device YES which will facilitate the discarding of pins and other examples which demonstrate why pins are not discarded.