With the recent DLC and update, and newly acquired vendor or queens wrath weapons (when equipped) can be reforged at the gunsmith in exchange for motes of light, weapon parts, and glimmer. The reforge option will reset and upgrade progress on the weapon, but will give you the chance to obtain perks on a weapon that you prefer. For example, I obtained a hand cannon from crucible, it came with outlaw and final round, as well as an optional perk tree I didn't like, so I brought it to the gunsmith and gave him 1 mote of light, 20 weapon parts, and 200 glimmer, about 15 times, till the hand cannon had final round, luck in the chamber, and small bore.