First, please check with the oscilloscope and make sure that all supply voltages for the GPS module, including the 3.15V VCC voltage on the pin 11, 1.5V V_BCKP voltage on the pin 5 and 3.15V antenna supply voltage on the RF connector are in place. Then, during initial power-up, cycle (assert and then de-assert back) the GPS_RESET_B signal for at least 1s.
I've not been able to start the GPS module on my i.MX6Q SABRE SD board so far, but on the i.MX53 SABRE SD board, that uses the same AH-1613 GPS module, I noticed that the module waits for some input from the host, possibly, to synchronize its UART port speed to the host UART port speed. On the i.MX53 SABRE SD board, the host sends the 0xAA 0x6A sequence of bytes, and only after that the GPS module starts sending some data. Please try it. Then, the host continuously sends the data to the GPS module, mostly, the all zero bytes. By the way, the host communicates to the GPS module at 115200bps speed on the i.MX53 SABRE SD board.
Regarding the custom configuration input to the AH-1613 module, its Data Sheet document (see attached) suggests to refer to the documentation of the Atheros AR1520A GPS chip, which the module is based on. However, the links below are the only things on this matter I've been able to find in public access so far:
http://wenku.baidu.com/view/357b6622482fb4daa58d4b26.html
http://wenku.baidu.com/view/764212fdf705cc1755270990.html
Have a great day,
Artur
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