Weapons are incredibly easy to convert over to MiniSix. Most are simply represented by their damage dice - not only is ammo not a problem for Rogue Trader characters (being that you can afford to buy a manufactorum to make all the ammo you'll ever need), but MiniSix's cinematic feel means that reloading isn't a massive concern.
Weapons are split into several "categories", each with its own Skill. Usually, possessing the appropriate Skill will allow a character to use that particular type of weapon, though GMs may over-rule this for certain types of weapons (Exotic ones in particular - while a pistol-shaped, pistol-like Archaeotech device may be usable under the Pistols Skill, an Eldar Shard Pistol might need a Skill dedicated to its use).
The damage ratings for each of these weapons correspond to firing either a single shot (for pistols, rifles, etc) or for firing a single burst (auto-weapons, stubbers etc). Weapons which can fire on fully automatic can fire multiple bursts, trading a die on the to-hit roll for a die of damage, to a maximum of 3 dice (so, an autogun can fire three bursts on "full auto", at -3D to hit, for an extra 3D damage).
Knife - +1D
Sword - +2D+2
Axe - +3D
Chain - +1D
Power - +2D, has a 70% chance to break non-Powered weapons on a successful Parry (or automatically if the Wild Die shows 6).
Force - add half the user's Psy Rating (rounded up) to the dice total (so, a Psyker with Psy Rating 3 will wield a Force Sword as a +4D+2 weapon).
Laspistol - 3D+2
Hellpistol - 4D+2, discard the lowest dice
Stub Gun - 3D
Hand Cannon - 4D
Autopistol - 3D+2
Shot-pistol - 4D+1
Bolt Pistol - 5D
Lasgun - 4D
Hellgun - 5D, discard the lowest
Lascarbine - 3D+2, can be used one-handed
Long-las - 5D
Autogun - 5D
Shotgun - 4D+2
Boltgun - 6D
Heavy Bolter - 4D, Scale +4D/+12
Lascannon - 5D, Scale +4D/+12
Autocannon - 5D, Scale +2D/6
Heavy Stubber - 6D
Melta + Plasma
Inferno Pistol - 7D
Meltagun - 7D, Scale +2D/+6
Thermal Lance - 7D+2, Scale +2D/+6
Multi-melta - 6D, Scale +4D/+12
Plasma pistol 7D
Plasma cannon - 4D, Scale +4D/+12
These numbers are mostly taken straight from Arkat's previous thread on RPG.net, so kudos to him for allowing me to reprint them here. Some might be changed after some playtesting.