The most accurate way will be to use FRET system, specially cost-effective if you are doing small number of probes or large number of samples. This system will accurately tell you if the normal or mutated variant is present. For this, the SNP needs to be located at the boundary of both probes.

If cost is too high for your budget, he standard way will be to use specific probes and enzymatic detection. For this, I have seen that most probes that work have the SNP towards the center of the probe, but you will have to do some trial and error to be able to find the best signal-to-noise result.

I hope this helps. If need any additional information, I'll be glad to help.

Good Luck!

Dear Marcos

Thanks for the advice. FRET system is new to me but looks like the method that's is appropriate to me as I have less probes and more samples. I will read about it and get back to you for further queries. Kindly share if you have any good papers about FRET system.

Regards

Pranay