5.4.5. FPGA Programming over External Intel® FPGA Download Cable
The JTAG chain header provides another method for configuring the FPGA using an external Intel® FPGA Download Cable device with the Quartus® Prime Programmer running on a PC. To prevent contention between the JTAG masters, the onboard Intel® FPGA Download Cable is automatically disabled when you connect an external Intel® FPGA Download Cable to the JTAG chain through the JTAG chain header.