PCI-e jtag interface
While the PCIe connector does have a few pins designated for JTAG, they are virtually never used. In particular, they are never connected to anything on PC motherboards.

If you want to program devices over JTAG, you will need to purchase a JTAG adapter -- these are typically USB devices. The JTAG functionality defined on the PCIe connector will not be of any help to you.