Hello Waqas,

1. Standard PCR. Design separate PCR primers whose target sequences are the breakpoints for the wild-type and the inversion, respectively, and then test in the lab. If the inversion is a false-positive, then the primers for the inversion should not amplify any sequence.
2. MLPA. You could also set-up an experiment using MLPA (Multiplex ligation-dependent probe amplification), where the probes target the breakpoint
3. Real-time PCR. Design common PCR primers outside of the breakpoint but make the probe sequences specific for the breakpoint in the wild-type and inversion.
4. Sanger. Also by designing common primers outside of the beakpoint, you could just do Sanger sequencing.

Finally, read this: Validation and Genotyping of Multiple Human Polymorphic Inversions Mediated by Inverted Repeats Reveals a High Degree of Recurrence .

Kevin