WhatsApp announced on its official Twitter handle that you can now make calls on the WhatsApp desktop. Use can make Whatsapp call from desktop like Skype. This feature will enable automatically for all users when you update to the latest version of WhatsApp.
To enable this feature update to the latest version of the application. Now open a chat and the options for audio and video calls will be displayed at the top.
Just make a call and the controls for managing the ongoing call will be displayed on the desktop. As you speak, you will see the change in the audio spectrum shown in the popup. This is how you can make Whatsapp calls from desktop.