I main Annie and Twisted Fate so I have Tier 3 runes for squishy caster.

I use:

Red: Magic pen
Yellow: Hp/lvl
Glyph: mana regen/5sec per lvl
Quin: HP

What should I change to make it good for Anivia?

Going by my guide, this is what I use for Anivia.

Red:Magic Pen
Yellow: Flat AP
Blue: AP/level
Quints:Flat AP

It'll be better with the next patch, as all AP runes are getting a buff by what the Test Realm notes say.

i use dodge for my yellows, that 7% chance to dodge is a life saver.