You have to set ViewController StoryBoardId property as below image.

open viewController using coding as below in swift

func application(application: UIApplication, didFinishLaunchingWithOptions launchOptions: [NSObject: AnyObject]?) -> Bool {


let mainStoryboardIpad : UIStoryboard = UIStoryboard(name: "Main", bundle: nil)
let initialViewControlleripad : UIViewController = mainStoryboardIpad.instantiateViewControllerWithIdentifier("Circles") as UIViewController
self.window = UIWindow(frame: UIScreen.main.bounds)
self.window?.rootViewController = initialViewControlleripad
self.window?.makeKeyAndVisible()


return true
}

For iOS 13+ (based on an article by dev2qa)
Open SceneDelegate.swift and add following

func scene(_ scene: UIScene, willConnectTo session: UISceneSession, options connectionOptions: UIScene.ConnectionOptions) {


// If this scene's self.window is nil then set a new UIWindow object to it.
self.window = self.window ?? UIWindow()


// Set this scene's window's background color.
self.window!.backgroundColor = UIColor.red


// Create a ViewController object and set it as the scene's window's root view controller.
self.window!.rootViewController = ViewController()


// Make this scene's window be visible.
self.window!.makeKeyAndVisible()


guard scene is UIWindowScene else { return }
}

There is an open-source navigation utility which attempts to make this easier. Example

First Initialize the window

self.window = UIWindow(frame: UIScreen.mainScreen().bounds)
let storyBoard = UIStoryboard(name: "Main", bundle: nil)

For setting rootViewController inside AppDelegate Class

let viewController = storyBoard.instantiateViewControllerWithIdentifier("Circles") as UIViewController
self.window?.rootViewController = viewController
self.window?.makeKeyAndVisible()

I'd say creating UIWindow each time you want to change rootViewController is bad idea. After couple changes of rootVC (using upper solution) you are gonna have many UIWindows in your app at one time.

In my opinion better solution is:

1. Get new rootVC: let rootVC = UIStoryboard(name: "StoryboardName", bundle: nil).instantiateViewControllerWithIdentifier("newRootVCIdentifier") as UIViewController
2. Set frame for new rootVC from UIScreen's bounds: rootVC.view.frame = UIScreen.mainScreen().bounds
3. Set new root controller for current window (here with animation): UIView.transitionWithView(self.window!, duration: 0.5, options: .TransitionCrossDissolve, animations: { self.window!.rootViewController = rootVC }, completion: nil)

Done!

You don't need method window?.makeKeyAndVisible(), cause this solution works on current app window.

Swift 3:

This is my preferred approach when presenting a new viewController from the current viewController through the AppDelegate. This way you don't have to completely tear down your view hierarchy when handling a push notification or universal link

if let controller = UIStoryboard(name: "Main", bundle: nil).instantiateViewController(withIdentifier: "someController") as? SomeController {
if let window = self.window, let rootViewController = window.rootViewController {
var currentController = rootViewController
while let presentedController = currentController.presentedViewController {
currentController = presentedController
}
currentController.present(controller, animated: true, completion: nil)
}
}

Swift 3

To present the view together with the navigation controller:

let storyboard = UIStoryboard(name: "Main", bundle: nil)
let viewController = storyboard.instantiateViewController(withIdentifier :"InboxViewController") as! InboxViewController
let navController = UINavigationController.init(rootViewController: viewController)


if let window = self.window, let rootViewController = window.rootViewController {
var currentController = rootViewController
while let presentedController = currentController.presentedViewController {
currentController = presentedController
}
currentController.present(navController, animated: true, completion: nil)
}

Swift 3 SWRevealViewController

    self.window = UIWindow(frame: UIScreen.main.bounds)
let storyBoard = UIStoryboard(name: "Main", bundle: nil)


let viewController = storyBoard.instantiateViewController(withIdentifier: "SWRevealViewController") as! SWRevealViewController
self.window?.rootViewController = viewController
self.window?.makeKeyAndVisible()

In Swift 3

        let mainStoryboard : UIStoryboard = UIStoryboard(name: StorybordName, bundle: nil)
let initialViewControlleripad : UIViewController = mainStoryboard.instantiateViewController(withIdentifier: identifierName) as UIViewController
if let navigationController = self.window?.rootViewController as? UINavigationController
{
navigationController.pushViewController(initialViewControlleripad, animated: animation)
}
else
{
print("Navigation Controller not Found")
}

let storyboard = UIStoryboard(name: "Main", bundle: nil)


let destinationViewController = storyboard.instantiateViewController(withIdentifier: "LandVC") as! LandingPageVC


destinationViewController.webpageURL = NotificationAdvertisement._htmlpackagePath
destinationViewController.adID = NotificationAdvertisement._adID
destinationViewController.toneID = NotificationAdvertisement.toneID


let navigationController = self.window?.rootViewController as! UIViewController


navigationController.showDetailViewController(destinationViewController, sender: Any?.self)

There is a swift 4 version

func application(_ application: UIApplication,
didFinishLaunchingWithOptions launchOptions:
[UIApplicationLaunchOptionsKey: Any]?) -> Bool {
let mainStoryboardIpad : UIStoryboard = UIStoryboard(name: "Main", bundle: nil)
let initialViewControlleripad : UIViewController = mainStoryboardIpad.instantiateViewController(withIdentifier: "Circles") as UIViewController
self.window = UIWindow(frame: UIScreen.main.bounds)
self.window?.rootViewController = initialViewControlleripad
self.window?.makeKeyAndVisible()


return true}

SWIFT 4

let storyboard = UIStoryboard(name: "Main", bundle: nil)


let destinationViewController = storyboard.instantiateViewController(withIdentifier: "LandVC") as! LandingPageVC


destinationViewController.webpageURL = NotificationAdvertisement._htmlpackagePath
destinationViewController.adID = NotificationAdvertisement._adID
destinationViewController.toneID = NotificationAdvertisement.toneID


let navigationController = self.window?.rootViewController as! UIViewController


navigationController.showDetailViewController(destinationViewController, sender: Any?.self)

func scene(_ scene: UIScene, willConnectTo session: UISceneSession, options connectionOptions: UIScene.ConnectionOptions) {
guard let windowScene = (scene as? UIWindowScene) else { return }
self.window = UIWindow(windowScene: windowScene)


let mainStoryboard : UIStoryboard = UIStoryboard(name: "Main", bundle: nil)
let vc : UIViewController = mainStoryboard.instantiateViewController(withIdentifier: "LoginViewController")
let rootNC = UINavigationController(rootViewController: vc)
self.window?.rootViewController = rootNC
self.window?.makeKeyAndVisible()


}