Bercause there are indeed quite a few ways of creating Exterminatus:
- Orbital Bombardment
Everyone and their's dog just start shooting down at the planet surface: nuclear warheads, battlebarge bombardment cannons, Nova cannons, Lance batteries and anything else big enough to glass the surface. It has been used by Dark Angels to destroy Caliban, Night Lords against Nostramo and during the purge of Typhon. Time-wise, this method is probably the least effective, but it is probably the one used in this case, since it doesn't ignite the planet atmosphere.
- Virus Bombing
Using an extremely aggressive Life-Eater virus that causes all living tissue to rot and decompose, which creates an immediate buildup of the flammable gases (This is probably the method that OP thinks about). After enough of the biological material has been decomposed, the atmosphere can be ignited (assuming it hasn't ignited itself already). This method has been used during the Great Crusade and Horus Heresy (i.e. at Istvaan Campaign against the loyalists), but currently it is not recommended since using it gives a massive power boost to Nurgle.
- Atmospheric Incineration Torpedo
A massive bombardment using plasma torpedoes that super-heat the atmosphere until all combustible materials ignite, turning the surface into a one, raging firestorm. It has been used to destroy Medusa IV, but in general, it is a costly method that can be used only on planets with a stable, flammable atmosphere.
- Modalis Atmospheric Missle
Similar to the previous method, but using the phosphex missiles, a material similar to white phosphorus or Greek Fire: an extremely corrosive and flammable material that is almost impossible to extinguish. Phosphex weapons are rare and irreplaceable - a Tech-Priest who found an STC describing a process of creating them, after witnessing the horror they create, decided to destroy all data regarding their production.
- Cyclonic Torpedoes
The primary way of Exterminatus: Fleet launches a huge number of specially modified nuclear weapons, that exploding simultaneously create a larger, self-sustaining nuclear reaction, basically turning briefly the whole planet into a small star. Please note, that in the books the power of such torpedoes varies a lot - sometimes few dozens have to be used against a single hive city, sometimes one is large enough for a whole planet. This can be explained (in-universe) that the "cyclonic torpedo" is a generic name for "atomic bomb".
- Two-stage Cyclonic Torpedoes
In this method, the torpedoes first burrow themselves (using melta charge) through the crust to the core of the planet before exploding. This doesn't as much "glass" the planet but cracks it in the Death Star style. This is the only way to deal with Necron Tomb worlds, that are hidden deep under the surface.
- Asteroid impact
Rarely used method that requires changing the orbit of a large asteroid (or even a moon) to collide with the planet. While efficient, it is horribly expensive and time-consuming, hence not recommended. It has been used in the Badab War and during the Horus Heresy when renegade Iron Hands destroyed the World Eaters world of Bodt.
Non-Imperial examples:
Eldar/Dark Eldar
Their strongest weapons were the Blackstone Fortresses, originally used to fight the C'Tan, that are able to turn stars into a supernova. Unfortunately, they are no longer in control of those devices, but they have the "Fireheart" - a psychic controlled weapon similar to the Cyclonic Torpedoes. There are also rumours, that the Cabal of the Dying Suns has weapons able to extinguish suns.
Necron
Besides the planet-size World Engine ship, they can supercharge solar flares on the star, that will fry the day-side of any planet in the system, or simply point to a star using the Celestial Orrery (arguably, the most powerful weapon in the whole universe!) which would turn the star nova. They can also just simply release a C'tan shard on the target planet.
Tyranids
Tyranids ARE exterminatus.
