Do like Active says. GFCI breakers won't work with a shared neutral but GFCI receptacles can be put on the two circuits after the neutral splice. Don't feel too bad ... many years ago I pulled 3 conductors thru 100 feet of 3/4 EMT and put GFCI breakers on it. That wasn't as bad as the fact that it took me 2 hours to realize why it didn't work. My old boss is still laughing at me.
I suppose that I failed to mention that the three wire goes to split outlets, many of them. However, even if I replaced each one with a GFR, it would be less expensive than a breaker. I was hoping to find an alternative . . .
As to why not make it one circuit, the owner wanted two circuits on each side of the garage one on the top of each outlet one on the bottom. Four 20A outlet circuits total, and independent of the lights too.