Beginning with Intel Quartus Prime software version 15.1.1 and up to but not including version 17.1, the RX polarity inversion soft logic option is hidden in the PHY Characteristics tab of the Intel Arria 10 Hard IP for PCI Express GUI.  From Intel Quartus Prime software version 17.1 and later, this RX polarity inversion soft logic option is natively visible in the GUI.
Instructions to enable the hidden RX polarity inversion soft logic option.
Open the Intel Arria 10 Hard IP for PCI Express GUI Select the PHY Characteristics tab Right click on the Intel Arria 10 Hard IP for PCI Express banner and select Show Hidden Parameters Scroll down until you see the Enable rx_polarity inversion soft logic parameter and select it Do not modify any other hidden parameters Right click on the Intel Arria 10 Hard IP for PCI Express banner and select Hide Hidden Parameters (optional but recommended) Select Generate HDL